Multidimensional engineering of Saccharomyces cerevisiae for the efficient production of heme by exploring the cytotoxicity and tolerance of heme.

Heme has attracted considerable attention due to its indispensable biological roles and applications in healthcare and artificial foods. The development and utilization of edible microorganisms instead of animals to produce heme is the most promising method to promote the large-scale industrial production and safe application of heme. However, the cytotoxicity of heme severely restricts its efficient synthesis by microorganisms, and the cytotoxic mechanism is not fully understood. In this study, the effect of heme toxicity on Saccharomyces cerevisiae was evaluated by enhancing its synthesis using metabolic engineering. The results showed that the accumulation of heme after the disruption of heme homeostasis caused serious impairments in cell growth and metabolism, as demonstrated by significantly poor growth, mitochondrial damage, cell deformations, and chapped cell surfaces, and these features which were further associated with substantially elevated reactive oxygen species (ROS) levels within the cell (mainly H2O2 and superoxide anion radicals). To improve cellular tolerance to heme, 5 rounds of laboratory evolution were performed, increasing heme production by 7.3-fold and 4.2-fold in terms of the titer (38.9 mg/L) and specific production capacity (1.4 mg/L/OD600), respectively. Based on comparative transcriptomic analyses, 32 genes were identified as candidates that can be modified to enhance heme production by more than 20% in S. cerevisiae. The combined overexpression of 5 genes (SPS22, REE1, PHO84, HEM4 and CLB2) was shown to be an optimal method to enhance heme production. Therefore, a strain with enhanced heme tolerance and ROS quenching ability (R5-M) was developed that could generate 380.5 mg/L heme with a productivity of 4.2 mg/L/h in fed-batch fermentation, with S. cerevisiae strains being the highest producers reported to date. These findings highlight the importance of improving heme tolerance for the microbial production of heme and provide a solution for efficient heme production by engineered yeasts.

Involvement of 2-deoxyglucose-6-phosphate phosphatases in facilitating resilience against ionic and osmotic stress in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae DOG genes, DOG1 and DOG2, encode for 2-deoxyglucose-6-phosphate phosphatases. These enzymes of the haloacid dehalogenase superfamily are known to utilize the non-natural 2-deoxyglucose-6-phosphate as their substrate. However, their physiological substrate and hence their biological role remain elusive. In this study, we investigated their potential role as enzymes in biosynthesizing glycerol through an alternative pathway, which involves the dephosphorylation of dihydroxyacetone phosphate into dihydroxyacetone, as opposed to the classical pathway which utilizes glycerol 3-phosphate. Overexpression of DOG1 or DOG2 rescued the osmotic and ionic stress-sensitive phenotype of gpp1∆ gpp2∆ or gpd1∆ gpd2∆ mutants, both affected in the production of glycerol. While small amounts of glycerol were observed in the DOG overexpression strains in the gpp1∆ gpp2∆ background, no glycerol was detected in the gpd1∆ gpd2∆ mutant background. This indicates that overexpression of the DOG enzymes can rescue the osmosensitive phenotype of the gpd1∆ gpd2∆ mutant independent of glycerol production. We also did not observe a drop in glycerol levels in the gpp1∆ gpp2∆ dog1∆ dog2∆ as compared to the gpp1∆ gpp2∆ mutant, indicating that the Dog enzymes are not involved in glycerol biosynthesis. This indicates that Dog enzymes have a distinct substrate and their function within the cell remains undiscovered. IMPORTANCE: Yeast stress tolerance is an important characteristic that is studied widely, not only regarding its fundamental insights but also for its applications within the biotechnological industry. Here, we investigated the function of two phosphatase encoding genes, DOG1 and DOG2, which are induced as part of the general stress response pathway, but their natural substrate in the cells remains unclear. They are known to dephosphorylate the non-natural substrate 2-deoxyglucose-6-phosphate. Here, we show that overexpression of these genes overcomes the osmosensitive phenotype of mutants that are unable to produce glycerol. However, in these overexpression strains, very little glycerol is produced indicating that the Dog enzymes do not seem to be involved in a previously predicted alternative pathway for glycerol production. Our work shows that overexpression of the DOG genes may improve osmotic and ionic stress tolerance in yeast.

Altered S-AdenosylMethionine availability impacts dNTP pools in Saccharomyces cerevisiae.

Saccharomyces cerevisiae has long been used as a model organism to study genome instability. The SAM1 and SAM2 genes encode AdoMet synthetases, which generate S-AdenosylMethionine (AdoMet) from Methionine (Met) and ATP. Previous work from our group has shown that deletions of the SAM1 and SAM2 genes cause changes to AdoMet levels and impact genome instability in opposite manners. AdoMet is a key product of methionine metabolism and the major methyl donor for methylation events of proteins, RNAs, small molecules, and lipids. The methyl cycle is interrelated to the folate cycle which is involved in de novo synthesis of purine and pyrimidine deoxyribonucleotides (dATP, dTTP, dCTP, and dGTP). AdoMet also plays a role in polyamine production, essential for cell growth and used in detoxification of reactive oxygen species (ROS) and maintenance of the redox status in cells. This is also impacted by the methyl cycle's role in production of glutathione, another ROS scavenger and cellular protectant. We show here that sam2∆/sam2∆ cells, previously characterized with lower levels of AdoMet and higher genome instability, have a higher level of each dNTP (except dTTP), contributing to a higher overall dNTP pool level when compared to wildtype. Unchecked, these increased levels can lead to multiple types of DNA damage which could account for the genome instability increases in these cells.

The signal peptide of yeast killer toxin K2 confers producer self-protection and allows conversion into a modular toxin-immunity system.

Some microbial toxins also target the producer species itself, necessitating a means of self-protection. The M2 double-stranded RNA (dsRNA) killer virus in Saccharomyces cerevisiae contains a single open reading frame (ORF) encoding both the secreted pore-forming toxin K2 as well as a cognate immunity factor. Here, we show that expression of a 49-amino acid N-terminal peptide from the K2 precursor is both necessary and sufficient for immunity. This immunity peptide simultaneously functions as a signal peptide for toxin secretion and protects the cell against the cytotoxic K2 α subunit. The K2 toxin and immunity factor can be functionally separated into two ORFs, yielding a modular toxin-immunity system. This case further shows how a (signal) peptide can carry the potential for providing cellular protection against an antimicrobial toxin.

Research Progress of ARTP Mutagenesis Technology Based on Citespace Visualization Analysis.

Atmospheric and room temperature plasma (ARTP) mutagenesis technology has been developed rapidly in recent years because of its simple operation, safety, environmental friendliness, high mutation rate, and large mutation library capacity. It has been widely used in traditional fields such as food, agriculture, and medicine, and has been gradually applied in emerging fields such as environmental remediation, bioenergy, and microalgae utilization. In this paper, the Web of Science Core Collection (WOSCC) was used as the data source, and the keywords and core literature of ARTP mutagenesis technology were plotted by citespace software, and the research progress and research hotspots of ARTP mutagenesis technology were analyzed. Through citespace visualization analysis, it is concluded that the country with the largest number of studies is China, the institution with the largest number of studies is Jiangnan University, and the author of the most published papers is Jiangnan University. Through keyword analysis, it is concluded that the most widely used ARTP mutagenesis technology is fermentation-related majors, mainly for biosynthesis and microbial research at the molecular level. Among them, the most widely used microorganisms are Escherichia coli and Saccharomyces cerevisiae.

The response mechanism analysis of HMX1 knockout strain to levulinic acid in Saccharomyces cerevisiae.

Levulinic acid, a hydrolysis product of lignocellulose, can be metabolized into important compounds in the field of medicine and pesticides by engineered strains of Saccharomyces cerevisiae. Levulinic acid, as an intermediate product widely found in the conversion process of lignocellulosic biomass, has multiple applications. However, its toxicity to Saccharomyces cerevisiae reduces its conversion efficiency, so screening Saccharomyces cerevisiae genes that can tolerate levulinic acid becomes the key. By creating a whole-genome knockout library and bioinformatics analysis, this study used the phenotypic characteristics of cells as the basis for screening and found the HMX1 gene that is highly sensitive to levulinic acid in the oxidative stress pathway. After knocking out HMX1 and treating with levulinic acid, the omics data of the strain revealed that multiple affected pathways, especially the expression of 14 genes related to the cell wall and membrane system, were significantly downregulated. The levels of acetyl-CoA and riboflavin decreased by 1.02-fold and 1.44-fold, respectively, while the content of pantothenic acid increased. These findings indicate that the cell wall-membrane system, as well as the metabolism of acetyl-CoA and riboflavin, are important in improving the resistance of Saccharomyces cerevisiae to levulinic acid. They provide theoretical support for enhancing the tolerance of microorganisms to levulinic acid, which is significant for optimizing the conversion process of lignocellulosic biomass to levulinic acid.

Effects of postbiotic products from Saccharomyces cerevisiae fermentation on lactation performance, antioxidant capacities, and blood immunity in transition dairy cows.

This study aimed to evaluate the effects of dietary supplementation with different types of Saccharomyces cerevisiae fermentation products (SCFP) on lactational performance, metabolism, acute phase protein response, and antioxidant capacities in dairy cows from -21 to 56 d in milk (DIM). One hundred and 80 multiparous Holstein dairy cows were blocked by parity, expected calving date, pre-trial body condition score, and previous 305-d ME yield, and then randomly assigned to 1 of 3 dietary treatments: basal diet (CON; n = 60), basal diet supplemented with 40 g/d of SCFP1 (XPC; n = 60; XPC, Diamond V, Cedar Rapids, IA), and basal diet supplemented with 19 g/d of SCFP2 (NTK; n = 60, NutriTek®, Diamond V, Cedar Rapids, IA). Blood (n = 15, 13 and 12 in the CON, XPC and NTK groups, respectively) was sampled at -7 ± 3, + 3, + 7, + 21, and + 28 d, and milk samples (n = 19, 18 and 15 in the CON, XPC and NTK groups, respectively) was sampled during 1-8 wk from a subset of cows from -21 to 56 d relative to calving. Data were analyzed using the MIXED procedure in SAS (SAS Institute Inc.). All data were subjected to repeated measures ANOVA. Dietary treatment (TRT), time, and their interaction (TRT × time) were considered as fixed effects and cow as the random effect. Cows fed XPC and NTK had greater energy-corrected milk (ECM). Supplementing NTK increased milk fat content and yield, and 3.5% fat-corrected milk (FCM) yield compared with CON. Milk urea nitrogen (MUN) was lower in XPC cows than CON. SCFP supplementation decreased plasma ß-hydroxybutyrate (BHB), ceruloplasmin (CER), haptoglobin (HPT), and interleukin-1ß (IL-1ß) concentrations, whereas increased plasma phosphorus (P) concentrations. In addition, cows fed NTK showed lower creatinine (CR) and cortisol (COR) concentrations but increased plasma calcium (Ca) and myeloperoxidase (MPO) concentrations than those in the CON cows. In addition, cows fed NTK and XPC both had reduced plasma concentrations of serum amyloid-A (SAA) at 3 DIM of lactation compared with CON fed cows. Furthermore, SCFP cows had greater concentrations of plasma glucose (GLU) and calcium (Ca) than CON cows at 7 DIM, and greater concentrations of plasma phosphorus (P) at 21 DIM. Between different SCFP type fed groups, plasma concentrations of nonesterified fatty acids (NEFA), MDA, creatinine (CR), SAA, and HPT were lower in cows fed NTK compared with cows fed XPC at 7 DIM. Overall, our results indicate the potential benefits of supplementing SCFP in transition dairy cows by modulating immunity, liver metabolic function and supporting ECM yield. The results also suggest that NutriTek at 19 g/d appears to support the performance and health of dairy cows better compared with XPC at 40 g/d, based on improved metabolic and inflammatory status during the transition period.

The Volatile Compounds Change during Fermentation of Saccharina japonica Seedling.

It is important to eliminate the fishy odor and improve the aroma quality of seafood. In this study, the Saccharina japonica (S. japonica) seedling, which is a new food material, was investigated for the effects of fermentation with Saccharomyces cerevisiae (S. cerevisiae) through sensory evaluation, GC-MS, and odor activity value (OAV) analysis. GC-MS analysis revealed the presence of 43 volatile compounds in the unfermented S. japonica seedling, with 1-octen-3-ol, hexanal, and trans-2,4-decadienal identified as the main contributors to its fishy odor. After fermentation with S. cerevisiae, 26 volatile compounds were identified in the S. japonica seedling. Notably, the major malodorous fish compounds, including 1-octen-3-ol, hexanal and trans-2,4-decadienal, were no longer present. The results indicate that fermentation with S. cerevisiae is an effective method for removing fishy malodor compounds and enhancing the volatile components with fruity, sweet, green, and floral notes in the Saccharina japonica seedling. This process facilitates the elimination of fishy malodor and enhance the fruity, sweet, green, and floral notes of S. japonica seeding and other seaweeds.

Sequential Pulsed Light and Ultrasound Treatments for the Inactivation of Saccharomyces cerevisiae and PPO and the Retention of Bioactive Compounds in Sweet Lime Juice.

Designing a pasteurization con dition for sweet lime juice while ensuring microbial safety, enzymatic stability, and high nutritional quality is crucial for satisfying stakeholder demands. The present research investigates the effects of matrix pH, ultrasound treatments, and sequential pulsed light on the microbial population, enzyme activity, and bioactive chemicals in sweet lime juice. The sequential pulsed light (PL: 0.6-0.84 J/cm2) and ultrasound (US: 0.2-0.4 W/cm3) treatments for sweet lime juice were optimized using response surface methodology (RSM). A three-factor full factorial design was used for this purpose. The independent variables encompassed pH (X1), PL effective fluence (X2, J/cm2), and US intensity (X3, W/cm3). The responses assessed included the inactivation of Saccharomyces cerevisiae (Y1, log cfu/mL) and polyphenol oxidase (PPO: Y2 in %) and the retention of vitamin C (Y3, %). The polynomial models were optimized using numerical optimization to attain the maximum desirability value (0.89). The optimized PL + US sample (0.8 J/cm2 + 0.4 W/cm3, respectively) at pH 3.5 resulted in a 5-log cycle reduction in S. cerevisiae count and a 90% inactivation in PPO activity and retained 95% of its vitamin C content. This optimized sample underwent further analysis, including phenolic profiling, assessment of microbial cell morphology, and examination of enzyme conformational changes. After sequential pulsed-light (0.8 J/cm2) and ultrasound (0.4 W/cm3) treatments, yeast cells showed unusual structural changes, indicating additional targets besides membranes. Following PL + US treatment, the PPO composition changed to 2.7 ± 0.1% α-helix, 33.9 ± 0.3% ß-sheet, 1.4 ± 0.2% ß-turn, and 62 ± 0.7% random coil. Impressively, the optimized PL + US sample maintained a sensory acceptance level similar to that of the untreated sample.

Encapsulation of Cinnamaldehyde and Vanillin as a Strategy to Increase Their Antimicrobial Activity.

Many studies have suggested that the encapsulation of natural antimicrobials increases their antimicrobial activity. In this sense, the objective was to study the inactivation of microorganisms with encapsulated cinnamaldehyde and vanillin (E-CIN and E-VN), in comparison with the unencapsulated antimicrobials (CIN and VN) in protein beverages. Additionally, the microbial response was quantified through mathematical modeling. Cinnamaldehyde and vanillin were encapsulated using whey protein concentrate (WPC) as the encapsulating agent. The effectiveness at inactivating Escherichia coli, Listeria innocua, and Saccharomyces cerevisiae was evaluated in a protein-apple juice beverage during storage (4 °C). Encapsulation increased the effectiveness of cinnamaldehyde, reaching reductions of 1.8, 3.3, and 5.3 log CFU/mL in E. coli, L. innocua, and S. cerevisiae, respectively, while vanillin encapsulation had little effect on antimicrobial activity, reducing by 0.5, 1.4, and 1.1 log cycles, respectively. The combined treatments (E-CIN + E-VN) had an additive effect in reducing E. coli and a synergistic effect against S. cerevisiae. The Gompertz model was more versatile and better described the biphasic curves, whereas the Weibull model complemented the information regarding the spectrum of resistances within the microbial population. In conclusion, the encapsulation of cinnamaldehyde with WPC enhanced its activity. However, further studies are necessary to improve the antimicrobial activity of vanillin.

Fermented Grapevine Leaves: Potential Preserving Agent in Yogurt.

In this study, we monitored the fermentative process of Vitis vinifera L. leaves (grapevine), spontaneously or promoted by Saccharomyces cerevisiae, in both solid and liquid media. We also aimed to evaluate the effect on the bioactivity and shelf life of yogurt incorporating fermented and non-fermented grapevine leaves compared to yogurt produced with the preservative potassium sorbate. The results revealed that fermented grapevine leaf extracts increased their bioactive compounds and antioxidant activity, particularly in fermentations in a solid medium. In yogurt samples with incorporation extract from solid spontaneous fermentation and extract from solid yeast fermentation, even in small quantities, they exhibited higher levels of total phenols (1.94 and 2.16 mg GAE/g of yogurt, respectively) and antioxidant activity (5.30 and 5.77 mg TroloxE/g of yogurt; and 1.33 and 1.34 mg Fe(II)E/g of yogurt, respectively) compared to control yogurt (1.44 mg GAE/g of yogurt, 4.00 mg TroloxE/g of yogurt, and 1.01 mg Fe(II)E/g of yogurt). Additionally, yogurts supplemented with fermented grapevine leaves demonstrated the potential to inhibit microbial growth without impairing the multiplication of lactic acid bacteria.

Culturable yeast community associated with grape must and honey bees sampled from apiaries located in the vineyards.

AIM: In this study, we investigated culturable yeast community, present in grape must sampled from vineyards with apiaries on the borders, and in honey bees collected in these apiaries. METHODS AND RESULTS: To this aim, yeasts isolated from spontaneously fermented grapes randomly collected in two vineyards (P1 and P2) with apiaries on the borders (A1 and A2) were compared to those isolated from spontaneously fermented grapes collected from a vineyard without apiary (P4). At the same time, yeast community was analyzed on bees collected in each apiary placed in the vineyards, in comparison to yeasts isolated from an apiary (A3) located far from the vineyards. The analysis was performed for two consecutive years (2021 and 2022). The isolated yeasts were identified by restriction analysis of amplified ITS region, followed by sequencing of ITS fragment.Our research showed that the presence of apiaries seems to increase yeast counts of grape must, in particular of Saccharomyces cerevisiae; furthermore, the permanence of apiaries in the vineyards allowed the recovering of these yeasts also from bees. CONCLUSIONS: Our findings seem to corroborate the role of bees as vectors and reservoirs of oenologically relevant yeasts, such as a source of non-conventional yeasts with potential biotechnological applications.

Safety and efficacy of a feed additive consisting of Saccharomyces cerevisiae CNCM I-1079 for dogs and all other Canidae (Danstar Ferment AG).

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of Saccharomyces cerevisiae CNCM I-1079 as a zootechnical feed additive for dogs and all other Canidae. The additive is intended for use in feed for dogs and all other Canidae at a proposed minimum inclusion level of 1 × 109 CFU per kg of complete feed. Saccharomyces cerevisiae is considered by EFSA to be suitable for the qualified presumption of safety approach to safety assessment. Since the identity of the active agent has been clearly established and no concerns are expected from other components of the product, the additive is considered safe for the target species. Since the additive is intended to be used only in feed for dogs and other non-food-producing animals, an assessment of the safety for the consumer and the environment is not needed. The non-coated form of the additive was shown to be non-irritant to skin and eyes. No conclusion can be drawn on the eye irritation potential of the coated form of the additive due to the lack of data. The additive in both forms, should be considered a skin and respiratory sensitiser and any exposure through skin and respiratory tract is considered a risk. The Panel was not in the position to conclude on the efficacy of Saccharomyces cerevisiae CNCM I-1079 at the proposed conditions of use.

Efficient production of 22(R)-hydroxycholesterol via combination optimization of Saccharomyces cerevisiae.

22(R)-hydroxycholesterol (22(R)-HCHO) is a crucial precursor of steroids biosynthesis with various biological functions. However, the production of 22(R)-HCHO is expensive and unsustainable due to chemical synthesis and extraction from plants or animals. This study aimed to construct a microbial cell factory to efficiently produce 22(R)-HCHO through systems metabolic engineering. First, we tested 7-dehydrocholesterol reductase (Dhcr7s) and cholesterol C22-hydroxylases from different sources in Saccharomyces cerevisiae, and the titer of 22(R)-HCHO reached 128.30 mg L-1 in the engineered strain expressing Dhcr7 from Columba livia (ClDhcr7) and cholesterol 22-hydroxylase from Veratrum californicum (VcCyp90b27). Subsequently, the 22(R)-HCHO titer was significantly increased to 427.78 mg L-1 by optimizing the critical genes involved in 22(R)-HCHO biosynthesis. Furthermore, hybrid diploids were constructed to balance cell growth and 22(R)-HCHO production and to improve stress tolerance. Finally, the engineered strain produced 2.03 g L-1 of 22(R)-HCHO in a 5-L fermenter, representing the highest 22(R)-HCHO titer reported to date in engineered microbial cell factories. The results of this study provide a foundation for further applications of 22(R)-HCHO in various industrially valuable steroids.

Diet supplementation with Saccharomyces cerevisiae influences the electrophoretic parameters in blood in young Charolaise bulls.

Introduction: The objective of the research was to investigate the effect of Saccharomyces cerevisiae supplementation on some acute-phase proteins, haptoglobin and all electrophoretic parameters in young Charolaise bulls. Material and Methods: Sixty bulls were divided into two equal groups: the control group (CG) receiving the base diet without yeast supplementation and the diet supplementation group (YG) receiving the base diet with 5g of Saccharomyces cerevisiae supplementation. The base diet was total mixed ration allocated at 11.85 kg per animal per day. Blood samples were collected from all bulls on day 0 before the start of the diet supplementation, and on days 20 and 40 after the start. Total proteins, albumin, globulin fraction (α1-, α2-, ß1-, ß2- and γ-globulins), albumin: globulin ratio (A: G) and haptoglobin were determined. Results: Two-way analysis of variance showed a significant effect of the yeast feeding time on all studied parameters except α2-globulins in both groups. The YG showed a higher average concentration of total proteins, albumin and A: G and a lower average concentration of γ-globulins and haptoglobin than the CG. Conclusion: These results indicated the beneficial effect of the Saccharomyces cerevisiae on the inflammatory status of the young bulls, which showed an adequate response in serum levels of the acute-phase proteins tested.

Genome sequence data of Saccharomyces cerevisiae CBS 493.94.

Whole genome sequencing (WGS) and data concerning identity and safety for Saccharomyces cerevisiae CBS 493.94 are reported. This strain was isolated from a British brewery in 1958 and deposited at the CBS culture collection Westerdijk Fungal Biodiversity Institute under the accession number CBS 493.94. The long-reads sequencing data, obtained via PacBio Sequel, and short-reads data, via Illumina NovaSeq 6000, were deposited at NCBI under accession number PRJNA1044661. The hybrid assembly was made publicly available via Zenodo and NCBI. For strain identification, data from 18S rRNA, ANI dendrogram and Core Genome single nucleotide polymorphism (SNP) Tree showed that the present isolate belongs to the genus Saccharomyces, species cerevisiae. The potential genes of concern, e.g. antimycotic resestance genes, were not detected. This strain is commonly used as a feed additive for animal health improvement and the present data summarise the unambiguous identity and strain's FKS1 gene does not code for any amino acid variants of concern.

Distinct regions of its first intracellular loop contribute to the proper localization, transport activity and substrate-affinity adjustment of the main yeast K+ importer Trk1.

Trk1 is the main K+ importer of Saccharomyces cerevisiae. Its proper functioning enables yeast cells to grow in environments with micromolar amounts of K+. Although the structure of Trk1 has not been experimentally determined, the transporter is predicted to be composed of four MPM (transmembrane segment - pore loop - transmembrane segment) motifs which are connected by intracellular loops. Of those, in particular the first loop (IL1) is unique in its length; it forms more than half of the entire protein. The deletion of the majority of IL1 does not abolish the transport activity of Trk1. However IL1 is thought to be involved in the modulation of the transporter's functioning. In this work, we prepared a series of internally shortened versions of Trk1 that lacked various parts of IL1, and we studied their properties in S. cerevisiae cells without chromosomal copies of TRK genes. Using this approach, we were able to determine that both N- and C-border regions of IL1 are necessary for the proper localization of Trk1. Moreover, the N-border part of IL1 is also important for the functioning of Trk1, as its absence resulted in a decrease in the transporter's substrate affinity. In addition, in the internal part of IL1, we newly identified a stretch of amino-acid residues that are indispensable for retaining the transporter's maximum velocity, and another region whose deletion affected the ability of Trk1 to adjust its affinity in response to external levels of K+.

A random mutagenesis screen enriched for missense mutations in bacterial effector proteins.

To remodel their hosts and escape immune defenses, many pathogens rely on large arsenals of proteins (effectors) that are delivered to the host cell using dedicated translocation machinery. Effectors hold significant insight into the biology of both the pathogens that encode them and the host pathways that they manipulate. One of the most powerful systems biology tools for studying effectors is the model organism, Saccharomyces cerevisiae. For many pathogens, the heterologous expression of effectors in yeast is growth inhibitory at a frequency much higher than housekeeping genes, an observation ascribed to targeting conserved eukaryotic proteins. Abrogation of yeast growth inhibition has been used to identify bacterial suppressors of effector activity, host targets, and functional residues and domains within effector proteins. We present here a yeast-based method for enriching for informative, in-frame, missense mutations in a pool of random effector mutants. We benchmark this approach against three effectors from Legionella pneumophila, an intracellular bacterial pathogen that injects a staggering >330 effectors into the host cell. For each protein, we show how in silico protein modeling (AlphaFold2) and missense-directed mutagenesis can be combined to reveal important structural features within effectors. We identify known active site residues within the metalloprotease RavK, the putative active site in SdbB, and previously unidentified functional motifs within the C-terminal domain of SdbA. We show that this domain has structural similarity with glycosyltransferases and exhibits in vitro activity consistent with this predicted function.

On the coupling of intracellular K + ${{\rm{K}}}

We have investigated the interplay between glycolytic oscillations and intracellular K + ${{\rm{K}}}^{+}$ concentration in the yeast Saccharomyces cerevisiae. Intracellular K + ${{\rm{K}}}^{+}$ concentration was measured using the fluorophore potassium-binding benzofuranisophthalate (PBFI). We found that K + ${{\rm{K}}}^{+}$ is an essential ion for the occurrence of glycolytic oscillations and that intracellular K + ${{\rm{K}}}^{+}$ concentration oscillates synchronously with other variables such as nicotinamide adenine dinucleotide hydride (NADH), intracellular adenosine triphosphate (ATP), and mitochondrial membrane potential. We also investigated if glycolysis and intracellular K + ${{\rm{K}}}^{+}$ concentration oscillate in a number of yeast strains with mutations in K + ${{\rm{K}}}^{+}$ transporters in the plasma membrane, mitochondrial membrane and in the vacuolar membrane. Most of these strains are still capable of showing glycolytic oscillations, but two strains are not: (i) a strain with a deletion in the mitochondrial Mdm38p K + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ transporter and (ii) a strain with deletion of the late endosomal Nhx1p K + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ ( Na + ∕ H + ${\text{Na}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ ) transporter. In these two mutant strains intracellular K + ${{\rm{K}}}^{+}$ concentration seems to be low, indicating that the two transporters may be involved in transport of K + ${{\rm{K}}}^{+}$ into the cytosol. In the strain, Mdm38p Δ ${\rm{\Delta }}$ oscillations in glycolysis could be restored by addition of the K + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ exchange ionophore nigericin. Furthermore, in two nonoscillating mutant strains with a defective V-ATPase and deletion of the Arp1p protein the intracellular K + ${{\rm{K}}}^{+}$ is relatively high, suggesting that the V-ATPase is essential for transport of K + ${{\rm{K}}}^{+}$ out of the cytosol and that the cytoskeleton may be involved in binding K + ${{\rm{K}}}^{+}$ to reduce the concentration of free ion in the cytosol. Analyses of the time series of oscillations of NADH, ATP, mitochondrial membrane potential, and potassium concentration using data-driven modeling corroborate the conjecture that K + ${{\rm{K}}}^{+}$ ion is essential for the emergence of oscillations and support the experimental findings using mutant strains.

Oxidative effects of the human antifungal drug clotrimazole on the eucaryotic model organism Saccharomyces cerevisiae.

Clotrimazole is a type of antifungal medication developed from azole compounds. It exhibits several biological actions linked to oxidative stress. This study focuses on the oxidative effects of clotrimazole on the eukaryotic model yeast, Saccharomyces cerevisiae. Our results showed that although initial nitric oxide levels were above control in clotrimazole exposed cells, they showed decreasing tendencies from the beginning of incubation and dropped below control at 125 µM from the 60th min. The highest superoxide anion and hydrogen peroxide levels were 1.95- and 2.85-folds of controls at 125 µM after 15 and 60 min, respectively. Hydroxyl radical levels slightly increased throughout the incubation period in all concentrations and reached 1.3-fold of control, similarly at 110 and 125 µM in the 90th min. The highest level of reactive oxygen species was observed at 110 µM, 2.31-fold of control. Although NADH/NADPH oxidase activities showed similar tendencies for all conditions, the highest activities were found as 3.07- and 2.27-folds of control at 125 and 110 µM in the 15th and 30th min, respectively. The highest superoxide dismutase and catalase activities were 1.59- and 1.21-folds of controls at 110 µM clotrimazole in 30 and 90 min, respectively. While the drug generally induced glutathione-related enzyme activities, the ratios of glutathione to oxidized glutathione were above the control only at low concentrations of the drug. The levels of lipid peroxidation in all treated cells were significantly higher than the controls. The findings crucially demonstrate that this medicine can generate serious oxidative stress in organisms.