Enhancement of fermentation traits in industrial Baker's yeast for low or high sugar environments

Saccharomyces cerevisiae SPC-SNU 70-1 is a commercial diploid baking yeast strain valued for its excellent bread-making qualities, including superior leavening capabilities and the production of flavor-enhancing volatile organic acids. Despite its benefits, this strain faces challenges in fermenting both lean (low-sugar) and sweet (high-sugar) doughs. To address these issues, we employed the CRISPR/Cas9 genome editing system to modify genes without leaving any genetic scars. For lean doughs, we enhanced the yeast's ability to utilize maltose over glucose by deleting a gene involved in glucose repression. For sweet doughs, we increased glycerol production by overexpressing glycerol biosynthetic genes and optimizing redox balance, thereby improving the tolerence to osmotic stress during fermentation. Additionally, the glycerol-overproducing strain demonstrated enhanced freeze tolerance, and bread made from this strain exhibited improved storage properties. This study demonstrates the feasibility and benefits of using engineered yeast strains, created solely by editing their own genes without introducing foreign genes, to enhance bread making.

Unveiling the fitness of Saccharomyces cerevisiae strains for lignocellulosic bioethanol: a genomic exploration through fermentation stress tests

Lignocellulosic biomass holds significant promise as a substrate for bioethanol production, yet the financial viability of lignocellulosic fermentation poses challenges. The pre-treatment step needed for lignocellulosic substrates generates inhibitors that impede Saccharomyces cerevisiae growth, affecting the fermentation process and overall yield. In modern sugarcane-to-ethanol plants, a rapid succession of yeast strains occurs, with dominant strains prevailing. Therefore, yeast strains with both dominance potential and inhibitor tolerance are crucial towards the development of superior strains with industrial fitness. This study adopted a hybrid approach combining biotechnology and bioinformatics to explore a cluster of 20 S. cerevisiae strains, including industrial and oenological strains exhibiting diverse phenotypic features. In-depth genomic analyses focusing on gene copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) were conducted and compared with results from fermentation tests once inoculated in multiple strains kinetics under stressing conditions such as low nitrogen availability and high formic or acetic acid levels. Some strains showed high resistance to biotic stress and acetic acid. Moreover, four out of 20 strains - namely S. cerevisiae YI30, Fp89, Fp90 and CESPLG05 - displayed promising resistance also to formic acid, the most impactful weak acids in pre-treated lignocellulosic biomass. These strains have the potential to be used for the development of superior S. cerevisiae strains tailored for lignocellulosic bioethanol production.

Encapsulation of Saccharomyces spp. for Use as Probiotic in Food and Feed: Systematic Review and Meta-analysis

Probiotics, particularly yeasts from the genus Saccharomyces, are valuable for their health benefits and potential as antibiotic alternatives. To be effective, these microorganisms must withstand harsh environmental conditions, necessitating advanced protective technologies such as encapsulation to maintain probiotic viability during processing, storage, and passage through the digestive system. This review and meta-analysis aims to describe and compare methods and agents used for encapsulating Saccharomyces spp., examining operating conditions, yeast origins, and species. It provides an overview of the literature on the health benefits of nutritional yeast consumption. A bibliographic survey was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. The meta-analysis compared encapsulation methods regarding their viability after encapsulation and exposure to the gastrointestinal tract. Nineteen studies were selected after applying inclusion/exclusion criteria. Freeze drying was found to be the most efficient for cell survival, while ionic gelation was best for maintaining viability after exposure to the gastrointestinal tract. Consequently, the combination of freeze drying and ionic gelation proved most effective in maintaining high cell viability during encapsulation, storage, and consumption. Research on probiotics for human food and animal feed indicates that combining freeze drying and ionic gelation effectively protects Saccharomyces spp.; however, industrial scalability must be considered. Reports on yeast encapsulation using agro-industrial residues as encapsulants offer promising strategies for preserving potential probiotic yeasts, contributing to the environmental sustainability of industrial processes.

Ppn2 Polyphosphatase Improves the Ability of S. cerevisiae to Grow in Mild Alkaline Medium

Inorganic polyphosphates and respective metabolic pathways and enzymes are important factors for yeast active growth in unfavorable conditions. However, particular proteins of polyphosphate metabolism remain poorly explored in this context. Here we report biochemical and transcriptomic characterization of the CRN/PPN2 yeast strain (derived from Ppn1-lacking CRN strain) overexpressing poorly studied Ppn2 polyphosphatase. We showed that Ppn2 overexpression significantly reduced lag phase in the alkaline medium presumably due to the ability of Ppn2 to efficiently hydrolyze inorganic polyphosphates and thus neutralize hydroxide ions in the cell. With RNA-Seq, we compared the molecular phenotypes of CRN/PPN2 and its parent CRN strain grown in YPD or alkaline medium and detected transcriptomic changes induced by Ppn2 overexpression and reflecting the adaptation to alkaline conditions. The core set of upregulated genes included several genes with a previously unknown function. Respective knockout strains (∆ecm8, ∆yol160w, ∆cpp3, ∆ycr099c) exhibited defects of growth or cell morphology in the alkaline medium, proving the functional involvement of the respective proteins in sustaining growth in alkaline conditions.

Enhancing freeze-thaw tolerance in baker's yeast: strategies and perspectives

Frozen dough technology is important in modern bakery operations, facilitating the transportation of dough at low temperatures to downstream sales points. However, the freeze-thaw process imposes significant stress on baker's yeast, resulting in diminished viability and fermentation capacity. Understanding the mechanisms underlying freeze-thaw stress is essential for mitigating its adverse effects on yeast performance. This review delves into the intricate mechanisms underlying freeze-thaw stress, focusing specifically on Saccharomyces cerevisiae, the primary yeast used in baking, and presents a wide range of biotechnological approaches to enhance freeze-thaw resistance in S. cerevisiae. Strategies include manipulating intracellular metabolites, altering membrane composition, managing antioxidant defenses, mediating aquaporin expression, and employing adaptive evolutionary and breeding techniques. Addressing challenges and strategies associated with freeze-thaw stress, this review provides valuable insights for future research endeavors, aiming to enhance the freeze-thaw tolerance of baker's yeast and contribute to the advancement of bakery science.

Key role of K+ and Ca2+ in high-yield ethanol production by S. Cerevisiae from concentrated sugarcane molasses

BACKGROUND

Saccharomyces cerevisiae is an important microorganism in ethanol synthesis, and with sugarcane molasses as the feedstock, ethanol is being synthesized sustainably to meet growing demands. However, high-concentration ethanol fermentation based on high-concentration sugarcane molasses-which is needed for reduced energy consumption of ethanol distillation at industrial scale-is yet to be achieved.

RESULTS

In the present study, to identify the main limiting factors of this process, adaptive laboratory evolution and high-throughput screening (Py-Fe3+) based on ARTP (atmospheric and room-temperature plasma) mutagenesis were applied. We identified high osmotic pressure, high temperature, high alcohol levels, and high concentrations of K+, Ca2+, K+ and Ca2+ (K+&Ca2+), and sugarcane molasses as the main limiting factors. The robust S. cerevisiae strains of NGT-F1, NGW-F1, NGC-F1, NGK+, NGCa2+ NGK+&Ca2+-F1, and NGTM-F1 exhibited high tolerance to the respective limiting factor and exhibited increased yield. Subsequently, ethanol synthesis, cell morphology, comparative genomics, and gene ontology (GO) enrichment analysis were performed in a molasses broth containing 250 g/L total fermentable sugars (TFS). Additionally, S. cerevisiae NGTM-F1 was used with 250 g/L (TFS) sugarcane molasses to synthesize ethanol in a 5-L fermenter, giving a yield of 111.65 g/L, the conversion of sugar to alcohol reached 95.53%. It is the highest level of physical mutagenesis yield at present.

CONCLUSION

Our results showed that K+ and Ca2+ ions primarily limited the efficient production of ethanol. Then, subsequent comparative transcriptomic GO and pathway analyses showed that the co-presence of K+ and Ca2+ exerted the most prominent limitation on efficient ethanol production. The results of this study might prove useful by promoting the development and utilization of green fuel bio-manufactured from molasses.

Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis

Significance: Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm. Recent Advances: Recent advancements in the study of photosynthesis have offered significant insights at the molecular level and with high temporal resolution into how the photosystem II oxygen-evolving complex manages to prevent harmful ROS production during the water-splitting process. These findings suggest that a dynamic spatiotemporal arrangement of redox reactions, coupled with strict regulation of proton transfer, is crucial for minimizing unnecessary ROS formation. Critical Issues: To better understand the multifaceted nature of these reactive molecular species in biology, it is worth considering a more holistic view that combines ecological and evolutionary perspectives on ROS, RNS, and RSS. By integrating spatiotemporal perspectives into global, cellular, and biochemical events, we discuss local pH or proton availability as a critical determinant associated with the generation and action of ROS, RNS, and RSS in biological systems. Future Directions: The concept of localized proton availability will not only help explain the multifaceted nature of these ubiquitous simple molecules in diverse systems but also provide a basis for new therapeutic strategies to manage and manipulate these reactive species in neural disorders, pathogenic diseases, and antiaging efforts.

Specific antioxidant enzymes are involved in the freeze-thawing response of industrial baker's yeasts

In this study, the biochemical basis of resistance to slow freezing and thawing (F-T) stress was explored in two baker yeast industrial strains of Saccharomyces cerevisiae that presented differential tolerance to freezing in order to be in the frozen bakery industry. Strain Y8, used commercially in sweet baking doughs, exhibited greater stress tolerance than Y9, a strain employed in regular doughs. Survival of Y8 was higher than that of Y9 (30% vs 12%) after F-T or other reactive oxygen species (ROS) inducing stresses compared to their non-stressed controls. The superior F-T tolerance of Y8 was related to its lower ROS accumulation capacity, determined by fluorometry in cell-free extracts and in vivo, by fluorescence microscopy upon F-T, being Y8 ROS accumulation 2-fold lower than that of Y9. That, in turn, could be positively associated with Y8's higher constitutive activities of cytosolic catalase (CAT) and superoxide dismutase by a significant activation (25%) of Y8 CAT after F-T. That would complement the protective effects of other protectant molecules like trehalose, present at high concentration in this strain.

The impacts of nicotinamide and inositol on the available cells and product performance of industrial baker's yeasts

A suitable nutrient supply, especially of vitamins, is very significant for the deep display of the inherent genetic properties of microorganisms. Here, using the chemically defined minimal medium (MM) for yeast, nicotinamide and inositol were confirmed to be more beneficial for the performance of two industrial baker's yeasts, a conventional and a high-sugar-tolerant strain. Increasing nicotinamide or inositol to proper levels could enhance the both strains on cell growth and activity and product performance, including trehalose accumulation and leavening performance. The activity of key enzymes (PCK, TPS) and the content of intermediate metabolites (G6P, UDPG) in the trehalose synthesis pathway were promoted by a moderate supply of nicotinamide and inositol. That were also proved that an appropriate amount of niacinamide promoted the transcription of longevity-related genes (PNC1, SIR2), and the proper concentration of inositol altered the phospholipid composition in cells, namely, phosphatidylinositol and phosphatidyl choline. Furthermore, the cell growth and the leavening performance of the both strains were promoted after adjusting inositol to choline to the proper ratio, resulting directly in content changes of phosphatidylinositol and phosphatidyl choline in the cells. While the two strains responded to the different proper ratio of inositol to choline probably due to their specific physiological characteristics. Such beneficial effects of increased nicotinamide levels were confirmed in natural media, molasses and corn starch hydrolyzed sugar media. Meanwhile, such adjustment of inositol to choline ratio could lessen the inhibition of excess inositol on cell growth of the two tested strains in corn starch hydrolyzed sugar media. However, in molasse, such phenomenon was not observed probably since there was higher Ca2+ in it. The results indicated that the effects of nutrient factors, such as vitamins, on cell growth and other properties found out from the simple chemically defined minimal medium were an effective measure to use in improving the recipe of natural media at least for baker's yeast.

Study of the Fermentation Characteristics of Non-Conventional Yeast Strains in Sweet Dough

Despite the diverse functions of yeast, only a relatively homogenous group of Saccharomyces cerevisiae yeasts is used in the baking industry. Much of the potential of the natural diversity of yeasts has not been explored, and the sensory complexity of fermented baked foods is limited. While research on non-conventional yeast strains in bread making is increasing, it is minimal for sweet fermented bakery products. In this study, the fermentation characteristics of 23 yeasts from the bakery, beer, wine, and spirits industries were investigated in sweet dough (14% added sucrose w/w dm flour). Significant differences in invertase activity, sugar consumption (0.78-5.25% w/w dm flour), and metabolite (0.33-3.01% CO₂; 0.20-1.26% ethanol; 0.17-0.80% glycerol; 0.09-0.29% organic acids) and volatile compound production were observed. A strong positive correlation (R² = 0.76, p < 0.001) between sugar consumption and metabolite production was measured. Several non-conventional yeast strains produced more positive aroma compounds and fewer off-flavors than the reference baker's yeast. This study shows the potential of non-conventional yeast strains in sweet dough.

Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics

Although various yeast strains used in the food industry have been characterized by multilayer analysis, knowledge of the variation of lipid profiles involved in fermentation characteristics and stress tolerance remains in its infancy. In this study, untargeted lipidomics was applied to 10 yeast strains, including laboratory, baker's, wine, and sake yeasts, which exhibit distinct fermentation phenotypes, to obtain a comprehensive overview of the yeast lipidome. The relative standard deviation (RSD) in the abundance of the 352 identified lipid molecular species was investigated to reveal the specific and common lipids. Lipids containing very long-chain fatty acids and hydroxy long-chain fatty acids showed relatively large RSD, whereas lipids containing acyl chains, which are commonly found in yeast, such as C16-C18, showed less RSD among the 10 strains. Furthermore, principal component analysis of lipid profiles showed similar trends among industrial yeast strains. As lipids are involved in yeast phenotypes, including stress tolerance and fermentation characteristics, correlation analysis was performed with lipid abundance and phenotypes. The results revealed that molecular species with a high RSD in abundance among the 10 strains were correlated with specific stress tolerance and fermentation phenotypes.

Using Kinetic Modelling to Infer Adaptations in Saccharomyces cerevisiae Carbohydrate Storage Metabolism to Dynamic Substrate Conditions

Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial bioreactors is still not understood mechanistically. To study the adjustments to prolonged dynamic conditions, we used published repeated substrate perturbation regime experimental data, extended it with proteomic measurements and used both for modelling approaches. Multiple types of data were combined; including quantitative metabolome, ¹³C enrichment and flux quantification data. Kinetic metabolic modelling was applied to study the relevant intracellular metabolic response dynamics. An existing model of yeast central carbon metabolism was extended, and different subsets of enzymatic kinetic constants were estimated. A novel parameter estimation pipeline based on combinatorial enzyme selection supplemented by regularization was developed to identify and predict the minimum enzyme and parameter adjustments from steady-state to dynamic substrate conditions. This approach predicted proteomic changes in hexose transport and phosphorylation reactions, which were additionally confirmed by proteome measurements. Nevertheless, the modelling also hints at a yet unknown kinetic or regulation phenomenon. Some intracellular fluxes could not be reproduced by mechanistic rate laws, including hexose transport and intracellular trehalase activity during substrate perturbation cycles.

Deletion of NTH1 and HSP12 increases the freeze–thaw resistance of baker’s yeast in bread dough

Background

The intracellular molecule trehalose in Saccharomyces cerevisiae may have a major protective function under extreme environmental conditions. NTH1 is one gene which expresses trehalase to degrade trehalose. Small heat shock protein 12 (HSP12 expressed) plays a role in protecting membranes and enhancing freezing stress tolerance.

Results

An optimized S. cerevisiae CRISPR-Cpf1 genome-editing system was constructed. Multiplex genome editing using a single crRNA array was shown to be functional. NTH1 or/and HSP12 knockout in S. cerevisiae enhanced the freezing stress tolerance and improved the leavening ability after freezing and thawing.

Conclusions

Deleting NTH1 in the combination with deleting HSP12 would strengthen the freezing tolerance and protect the cell viability from high rates of death in longer-term freezing. It provides valuable insights for breeding novel S. cerevisiae strains for the baking industry through a more precise, speedy, and economic genome-editing system.

A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation

Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.

Native SodB Overexpression of Synechocystis sp. PCC 6803 Improves Cell Growth Under Alcohol Stresses Whereas Its Gpx2 Overexpression Impacts on Growth Recovery from Alcohol Stressors

To overcome the limited resistance to alcohol stress, genetically engineered Synechocystis sp. PCC 6803 strains with overexpressions of genes related with the ROS detoxification system (sodB and gpx2, which encode superoxide dismutase and glutathione peroxidase, respectively) were developed. Three engineered strains including a sodB-overexpressing strain (OE + S), a gpx2-overexpressing strain (OE + G), and a sodB/gpx2-overexpressing strain (OE + SG) grew similarly as wild-type control under normal condition. When compared to wild-type control, OE + S and OE + SG strains grew faster for 4 days under 2.0% (v/v) ethanol and 0.3% (v/v) n-butanol conditions, as well as having higher chlorophyll a levels. On the other hand, the prominent growth recovery of OE + G and OE + SG was noted within 4 days in normal BG₁₁ medium after treating cells with high alcohol stresses for 1 h, in particular 15% ethanol and 2.5% n-butanol. Under 4 days of recovery from butanol stress, specific levels of intracellular pigments including chlorophyll a and carotenoids were dramatically increased in all modified strains. The overexpression of antioxidant genes then revealed a significant improvement of alcohol tolerance in Synechocystis sp. PCC 6803.

Intracellular trehalose accumulation via the Agt1 transporter promotes freeze-thaw tolerance in Saccharomyces cerevisiae

AIM

This study is to investigate the use of a constitutively expressed trehalose transport protein to directly control intracellular trehalose levels and protect baker's yeast (Saccharomyces cerevisiae) cells against freeze-thaw stress in vivo.

METHODS AND RESULTS

We used a constitutively overexpressed Agt1 transporter system to investigate the role of trehalose in the freeze-thaw tolerance of yeast cells by regulating intracellular trehalose concentrations independently of intracellular biosynthesis. Using this method, we found that increasing intracellular trehalose in yeast cells improved cell survival rate after 8 days of freezing at -80°C and -20°C. We also observed that freeze-thaw tolerance promoted by intracellular trehalose only occurs in highly concentrated cell pellets rather than cells in liquid suspension.

CONCLUSIONS

Trehalose is sufficient to provide freeze-thaw tolerance using our Agt1 overexpression system. Freeze-thaw tolerance can be further enhanced by deletion of genes encoding intracellular trehalose degradation enzymes.

SIGNIFICANCE AND IMPACT OF STUDY

These findings are relevant to improving the freeze-thaw tolerance of baker's yeast in the frozen baked goods industry through engineering strains that can accumulate intracellular trehalose via a constitutively expressed trehalose transporter and inclusion of trehalose into the growth medium.

Species-Dependent Metabolic Response to Lipid Mixtures in Wine Yeasts

Lipids are essential energy storage compounds and are the core structural elements of all biological membranes. During wine alcoholic fermentation, the ability of yeasts to adjust the lipid composition of the plasma membrane partly determines their ability to cope with various fermentation-related stresses, including elevated levels of ethanol and the presence of weak acids. In addition, the lipid composition of grape juice also impacts the production of many wine-relevant aromatic compounds. Several studies have evaluated the impact of lipids and of their metabolism on fermentation performance and aroma production in the dominant wine yeast Saccharomyces cerevisiae, but limited information is available on other yeast species. Thus, the aim of this study was to evaluate the influence of specific fatty acid and sterol mixtures on various non-Saccharomyces yeast fermentation rates and the production of primary fermentation metabolites. The data show that the response to different lipid mixtures is species-dependent. For Metschnikowia pulcherrima, a slight increase in carbon dioxide production was observed in media enriched with unsaturated fatty acids whereas Kluyveromyces marxianus fermented significantly better in synthetic media containing a higher concentration of polyunsaturated fatty acids than monounsaturated fatty acids. Torulaspora delbrueckii fermentation rate increased in media supplemented with lipids present at an equimolar concentration. The data indicate that these different responses may be linked to variations in the lipid profile of these yeasts and divergent metabolic activities, in particular the regulation of acetyl-CoA metabolism. Finally, the results suggest that the yeast metabolic footprint and ultimately the wine organoleptic properties could be optimized via species-specific lipid adjustments.

Yeast as a biological platform for vitamin D production: A promising alternative to help reduce vitamin D deficiency in humans

Vitamin D is an important human hormone, known primarily to be involved in the intestinal absorption of calcium and phosphate, but it is also involved in various non-skeletal processes (molecular, cellular, immune, and neuronal). One of the main health problems nowadays is the vitamin D deficiency of the human population due to lack of sun exposure, with estimates of one billion people worldwide with vitamin D deficiency, and the consequent need for clinical intervention (i.e., prescription of pharmacological vitamin D supplements). An alternative to reduce vitamin D deficiency is to produce good dietary sources of it, a scenario in which the yeast Saccharomyces cerevisiae seems to be a promising alternative. This review focuses on the potential use of yeast as a biological platform to produce vitamin D, summarizing both the biology aspects of vitamin D (synthesis, ecology and evolution, metabolism, and bioequivalence) and the work done to produce it in yeast (both for vitamin D₂ and for vitamin D₃ ), highlighting existing challenges and potential solutions. This article is protected by copyright. All rights reserved.

Molecular mechanisms and highly functional development for stress tolerance of the yeast Saccharomyces cerevisiae

In response to environmental stress, microorganisms adapt to drastic changes while exerting cellular functions by controlling gene expression, metabolic pathways, enzyme activities, and protein-protein interactions. Microbial cells that undergo a fermentation process are subjected to stresses, such as high temperature, freezing, drying, changes in pH and osmotic pressure, and organic solvents. Combinations of these stresses that continue over long terms often inhibit cells' growth and lead to their death, markedly limiting the useful functions of microorganisms (eg their fermentation ability). Thus, high stress tolerance of cells is required to improve productivity and add value to fermented/brewed foods and biofuels. This review focuses on stress tolerance mechanisms, including l-proline/l-arginine metabolism, ubiquitin system, and transcription factors, and the functional development of the yeast Saccharomyces cerevisiae, which has been used not only in basic science as a model of higher eukaryotes but also in fermentation processes for making alcoholic beverages, food products, and bioethanol.

Non-Conventional Yeasts as Alternatives in Modern Baking for Improved Performance and Aroma Enhancement

Saccharomyces cerevisiae remains the baker’s yeast of choice in the baking industry. However, its ability to ferment cereal flour sugars and accumulate CO2 as a principal role of yeast in baking is not as unique as previously thought decades ago. The widely conserved fermentative lifestyle among the Saccharomycotina has increased our interest in the search for non-conventional yeast strains to either augment conventional baker’s yeast or develop robust strains to cater for the now diverse consumer-driven markets. A decade of research on alternative baker’s yeasts has shown that non-conventional yeasts are increasingly becoming important due to their wide carbon fermentation ranges, their novel aromatic flavour generation, and their robust stress tolerance. This review presents the credentials of non-conventional yeasts as attractive yeasts for modern baking. The evolution of the fermentative trait and tolerance to baking-associated stresses as two important attributes of baker’s yeast are discussed besides their contribution to aroma enhancement. The review further discusses the approaches to obtain new strains suitable for baking applications.

Hsp104 contributes to freeze-thaw tolerance by maintaining proteasomal activity in a spore clone isolated from Shirakami kodama yeast

The supply of oven-fresh bakery products to consumers has been improved by frozen dough technology; however, freeze-thaw stress decreases the activity of yeast cells. To breed better baker's yeasts for frozen dough, it is important to understand the factors affecting freeze-thaw stress tolerance in baker's yeast. We analyzed the stress response in IB1411, a spore clone from Saccharomyces cerevisiae Shirakami kodama yeast, with an exceptionally high tolerance to freeze-thaw stress. Genes encoding trehalose-6-phosphate synthase (TPS1), catalase (CTT1), and disaggregase (HSP104) were highly expressed in IB1411 cells even under conditions of non-stress. The expression of Hsp104 protein was also higher in IB1411 cells even under non-stress conditions. Deletion of HSP104 (hsp104Δ) in IB1411 cells reduced the activity of the ubiquitin-proteasome system (UPS). By monitoring the accumulation of aggregated proteins using the ΔssCPY*-GFP fusion protein under freeze-thaw stress or treatment with proteasomal inhibitor, we found that IB1411 cells resolved aggregated proteins faster than the hsp104Δ strain. Thus, Hsp104 seems to contribute to freeze-thaw tolerance by maintaining UPS activity via the disaggregation of aggregated proteins. Lastly, we found that the IB1411 cells maintained high leavening ability in frozen dough as compared with the parental strain, Shirakami kodama yeast, and thus will be useful for making bread.

Preservation of non-Saccharomyces yeasts: Current technologies and challenges

There is a recent and growing interest in the study and application of non-Saccharomyces yeasts, mainly in fermented foods. Numerous publications and patents show the importance of these yeasts. However, a fundamental issue in studying and applying them is to ensure an appropriate preservation scheme that allows to the non-Saccharomyces yeasts conserve their characteristics and fermentative capabilities by long periods of time. The main objective of this review is to present and analyze the techniques available to preserve these yeasts (by conventional and non-conventional methods), in small or large quantities for laboratory or industrial applications, respectively. Wine fermentation is one of the few industrial applications of non-Saccharomyces yeasts, but the preservation stage has been a major obstacle to achieve a wider application of these yeasts. This review considers the preservation techniques, and clearly defines parameters such as culturability, viability, vitality and robustness. Several conservation strategies published in research articles as well as patents are analyzed, and the advantages and disadvantages of each technique used are discussed. Another important issue during conservation processes is the stress to which yeasts are subjected at the time of preservation (mainly oxidative stress). There is little published information on the subject for non-Saccharomyces yeast, but it is a fundamental point to consider when designing a preservation strategy.

Proteomic Analysis of Saccharomyces cerevisiae Response to Oxidative Stress Mediated by Cocoa Polyphenols Extract

The present study addressed the protective effects against oxidative stress (OS) of a cocoa powder extract (CPEX) on the protein expression profile of S. cerevisiae. A proteomic analysis was performed after culture preincubation with CPEX either without stress (−OS) or under stress conditions (+OS) (5 mM of H₂O₂). LC-MS/MS identified 33 differentially expressed proteins (–OS: 14, +OS: 19) that were included By Gene Ontology analysis in biological processes: biosynthesis of amino acids, carbohydrate metabolism and reactive oxygen species metabolic process. In a gene-knockout strains study, eight proteins were identified as putative candidates for being involved in the protective mechanism of cocoa polyphenols against OS induced by H₂O₂. CPEX was able to exert its antioxidant activity in yeast mainly through the regulation of: (a) amino acids metabolism proteins by modulating the production of molecules with known antioxidant roles; (b) stress-responsive protein Yhb1, but we were unable to fully understand its down-regulation; (c) protein Prb1, which can act by clipping Histone H3 N-terminal tails that are related to cellular resistance to DNA damaging agents.

Cryoprotective effect of silver carp muscle hydrolysate on baker's yeast Saccharomyces cerevisiae and its underlying mechanism

Cryoprotective effect of silver carp muscle hydrolysate (SCMH) on baker's yeast (Saccharomyces cerevisiae) was examined by analyzing the growth and survival of the yeast during freeze-thaw cycles, and the physicochemical properties [ultrastructure, intracellular proteins and fatty acids, external ice formation (EIF) and internal ice formation (IIF), freezable water content] of yeast cells with or without SCMH through transmission electron microscopy, SDS-PAGE, GC-MS, and differential scanning calorimetry. The 4% of SCMH treatment exhibited good yeast cryoprotective activity and increased the yeast survival rate from 0.71% to 90.95% after 1 freeze-thaw cycle as compared to the control. The results demonstrated that the addition of SCMH could attenuate the freeze damage of yeast cells, prevent the degradation or loss of soluble proteins, and increase the composition and absolute content of fatty acids. Besides, the addition of 4% SCMH caused a drop in the EIF peak temperature (from -17.95℃ to -25.14℃) and a decrease in the IIF and freezable water content of yeast cells.

Yeast Life Span and its Impact on Food Fermentations

Yeasts are very important microorganisms for food production. The high fermentative capacity, mainly of the species of the genus Saccharomyces, is a key factor for their biotechnological use, particularly to produce alcoholic beverages. As viability and vitality are essential to ensure their correct performance in industry, this review addresses the main aspects related to the cellular aging of these fungi as their senescence impacts their proper functioning. Laboratory strains of S. cerevisiae have proven a very successful model for elucidating the molecular mechanisms that control life span. Those mechanisms are shared by all eukaryotic cells. S. cerevisiae has two models of aging, replicative and chronological. Replicative life span is measured by the number of daughter cells a mother can produce. This kind of aging is relevant when the yeast biomass is reused, as in the case of beer fermentations. Chronological life span is measured by the time cells are viable in the stationary phase, and this is relevant for batch fermentations when cells are most of the time in a non-dividing state, such as wine fermentations. The molecular causes and pathways regulating both types of aging are explained in this review.

Metabolic regulatory mechanisms and physiological roles of functional amino acids and their applications in yeast

In yeast, amino acid metabolism and its regulatory mechanisms vary under different growth environments by regulating anabolic and catabolic processes, including uptake and export, and the metabolic styles form a complicated but robust network. There is also crosstalk with various metabolic pathways, products and signal molecules. The elucidation of metabolic regulatory mechanisms and physiological roles is important fundamental research for understanding life phenomenon. In terms of industrial application, the control of amino acid composition and content is expected to contribute to an improvement in productivity, and to add to the value of fermented foods, alcoholic beverages, bioethanol, and other valuable compounds (proteins and amino acids, etc.). This review article mainly describes our research in constructing yeast strains with high functionality, focused on the metabolic regulatory mechanisms and physiological roles of "functional amino acids", such as l-proline, l-arginine, l-leucine, l-valine, l-cysteine, and l-methionine, found in yeast.

Sodium Acetate Responses in Saccharomyces cerevisiae and the Ubiquitin Ligase Rsp5

Recent studies have revealed the feasibility of sodium acetate as a potentially novel inhibitor/stressor relevant to the fermentation from neutralized lignocellulosic hydrolysates. This mini-review focuses on the toxicity of sodium acetate, which is composed of both sodium and acetate ions, and on the involved cellular responses that it elicits, particularly via the high-osmolarity glycerol (HOG) pathway, the Rim101 pathway, the P-type ATPase sodium pumps Ena1/2/5, and the ubiquitin ligase Rsp5 with its adaptors. Increased understanding of cellular responses to sodium acetate would improve our understanding of how cells respond not only to different stimuli but also to composite stresses induced by multiple components (e.g., sodium and acetate) simultaneously. Moreover, unraveling the characteristics of specific stresses under industrially related conditions and the cellular responses evoked by these stresses would be a key factor in the industrial yeast strain engineering toward the increased productivity of not only bioethanol but also advanced biofuels and valuable chemicals that will be in demand in the coming era of bio-based industry.

Importance of Proteasome Gene Expression during Model Dough Fermentation after Preservation of Baker's Yeast Cells by Freezing

Freeze-thaw stress causes various types of cellular damage, survival and/or proliferation defects, and metabolic alterations. However, the mechanisms underlying how cells cope with freeze-thaw stress are poorly understood. Here, model dough fermentations using two baker's yeast strains, 45 and YF, of Saccharomyces cerevisiae were compared after 2 weeks of cell preservation in a refrigerator or freezer. YF exhibited slow fermentation after exposure to freeze-thaw stress due to low cell viability. A DNA microarray analysis of the YF cells during fermentation revealed that the genes involved in oxidative phosphorylation were relatively strongly expressed, suggesting a decrease in the glycolytic capacity. Furthermore, we found that mRNA levels of the genes that encode the components of the proteasome complex were commonly low, and ubiquitinated proteins were accumulated by freeze-thaw stress in the YF strain. In the cells with a laboratory strain background, treatment with the proteasome inhibitor MG132 or the deletion of each transcriptional activator gene for the proteasome genes (RPN4, PDR1, or PDR3) led to marked impairment of model dough fermentation using the frozen cells. Based on these data, proteasomal degradation of freeze-thaw-damaged proteins may guarantee high cell viability and fermentation performance. We also found that the freeze-thaw stress-sensitive YF strain was heterozygous at the PDR3 locus, and one of the alleles (A148T/A229V/H336R/L541P) was shown to possess a dominant negative phenotype of slow fermentation. Removal of such responsible mutations could improve the freeze-thaw stress tolerance and the fermentation performance of baker's yeast strains, as well as other industrial S. cerevisiae strains.IMPORTANCE The development of freezing technology has enabled the long-term preservation and long-distance transport of foods and other agricultural products. Fresh yeast, however, is usually not frozen because the fermentation performance and/or the viability of individual cells is severely affected after thawing. Here, we demonstrate that proteasomal degradation of ubiquitinated proteins is an essential process in the freeze-thaw stress responses of S. cerevisiae Upstream transcriptional activator genes for the proteasome components are responsible for the fermentation performance after freezing preservation. Thus, this study provides a potential linkage between freeze-thaw stress inputs and the transcriptional regulatory network that might be functionally conserved in higher eukaryotes. Elucidation of the molecular targets of freeze-thaw stress will contribute to advances in cryobiology, such as freezing preservation of human cells, tissues, and embryos for medical purposes and breeding of industrial microorganisms and agricultural crops that adapt well to low temperatures.

Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds

Development of the next-generation biocatalyst is vital for fermentation-based industrial applications and a sustainable bio-based economy. Overcoming the major class of toxic compounds associated with lignocellulose-to-biofuels conversion is one of the significant challenges for new strain development. A significant number of investigations have been made to understand mechanisms of the tolerance for industrial yeast. It is humbling to learn how complicated the cell's response to the toxic chemicals is and how little we have known about yeast tolerance in the universe of the living cell. This study updates our current knowledge on the tolerance of industrial yeast against aldehyde inhibitory compounds at cellular, molecular and the genomic levels. It is comprehensive yet specific based on reproducible evidence and cross confirmed findings from different investigations using varied experimental approaches. This research approaches a rational foundation toward a more comprehensive understanding on the yeast tolerance. Discussions and perspectives are also proposed for continued exploring the puzzle of the yeast tolerance to aid the next-generation biocatalyst development.

Gene expression profiles of Candida glycerinogenes under combined heat and high-glucose stresses

Low cell tolerance is a basic issue in high-glucose fermentation under high temperature to economically obtain high product titer. Candida glycerinogenes, an industrial yeast, has excellent tolerance to the combined heat and high-glucose stress than Saccharomycescerevisiae. The potential mechanism responsible for the high tolerance was illustrated here. The transcription of the potential stress-responsive genes in two strains were varied under single stress (heat or high-glucose), especially the ribosome-related genes. Unlike S. cerevisiae, C. glycerinogenes up-regulated 17 genes, including most of the single stress responsive genes, and genes Avt1 and Pfk1 under the combined stress, indicating a more systematic stress-responsive system in C. glycerinogenes. Further down-regulating the 17 potential key responsive genes indicated that genes Dip5, Gpd1, Pfk1, Hxt4, Hxt6, and Ino4 are important for cell tolerance to the combined stress. Furthermore, most of the ribosomal function related genes, such as Mrt4, Nug1, Nop53, Rpa190, Rex4, and Nsr1, play important role in cell tolerance. Therefore, the wider responsive gene spectrum and the activated expression of ribosomal function related genes might be key and prerequisite factors for the excellent tolerance to the combined stress of C. glycerinogenes.

Physiology, ecology and industrial applications of aroma formation in yeast

Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.

Improving freeze-tolerance of baker’s yeast through seamless gene deletion of NTH1 and PUT1

Baker’s yeast strains with freeze-tolerance are highly desirable to maintain high leavening ability after freezing. Enhanced intracellular concentration of trehalose and proline in yeast is linked with freeze-tolerance. In this study, we constructed baker’s yeast with enhanced freeze-tolerance by simultaneous deletion of the neutral trehalase-encoded gene NTH1 and the proline oxidase-encoded gene PUT1. We first used the two-step integration-based seamless gene deletion method to separately delete NTH1 and PUT1 in haploid yeast. Subsequently, through two rounds of hybridization and sporulation-based allelic exchange and colony PCR-mediated tetrad analysis, we obtained strains with restored URA3 and deletion of NTH1 and/or PUT1. The resulting strain showed higher cell survival and dough-leavening ability after freezing compared to the wild-type strain due to enhanced accumulation of trehalose and/or proline. Moreover, mutant with simultaneous deletion of NTH1 and PUT1 exhibits the highest relative dough-leavening ability after freezing compared to mutants with single-gene deletion perhaps due to elevated levels of both trehalose and proline. These results verified that it is applicable to construct frozen dough baker’s yeast using the method proposed in this paper.

MAL62 overexpression and NTH1 deletion enhance the freezing tolerance and fermentation capacity of the baker's yeast in lean dough

BACKGROUND

Trehalose is related to several types of stress responses, especially freezing response in baker's yeast (Saccharomyces cerevisiae). It is desirable to manipulate trehalose-related genes to create yeast strains that better tolerate freezing-thaw stress with improved fermentation capacity, which are in high demand in the baking industry.

RESULTS

The strain overexpressing MAL62 gene showed increased trehalose content and cell viability after prefermention-freezing and long-term frozen. Deletion of NTH1 in combination of MAL62 overexpression further strengthens freezing tolerance and improves the leavening ability after freezing-thaw stress.

CONCLUSIONS

The mutants of the industrial baker's yeast with enhanced freezing tolerance and leavening ability in lean dough were developed by genetic engineering. These strains had excellent potential industrial applications.

Enhanced leavening properties of baker's yeast by reducing sucrase activity in sweet dough

Leavening ability in sweet dough is required for the commercial applications of baker's yeast. This property depends on many factors, such as glycolytic activity, sucrase activity, and osmotolerance. This study explored the importance of sucrase level on the leavening ability of baker's yeast in sweet dough. Furthermore, the baker's yeast strains with varying sucrase activities were constructed by deleting SUC2, which encodes sucrase or replacing the SUC2 promoter with the VPS8/TEF1 promoter. The results verify that the sucrase activity negatively affects the leavening ability of baker's yeast strains under high-sucrose conditions. Based on a certain level of osmotolerance, sucrase level plays a significant role in the fermentation performance of baker's yeast, and appropriate sucrase activity is an important determinant for the leavening property of baker's yeast in sweet dough. Therefore, modification on sucrase activity is an effective method for improving the leavening properties of baker's yeast in sweet dough. This finding provides guidance for the breeding of industrial baker's yeast strains for sweet dough leavening. The transformants BS1 with deleted SUC2 genetic background provided decreased sucrase activity (a decrease of 39.3 %) and exhibited enhanced leavening property (an increase of 12.4 %). Such a strain could be useful for industrial applications.

Improvement of stress tolerance and leavening ability under multiple baking-associated stress conditions by overexpression of the SNR84 gene in baker's yeast

During the bread-making process, industrial baker's yeast cells are exposed to multiple baking-associated stresses, such as elevated high-temperature, high-sucrose and freeze-thaw stresses. There is a high demand for baker's yeast strains that could withstand these stresses with high leavening ability. The SNR84 gene encodes H/ACA snoRNA (small nucleolar RNA), which is known to be involved in pseudouridylation of the large subunit rRNA. However, the function of the SNR84 gene in baker's yeast coping with baking-associated stresses remains unclear. In this study, we explored the effect of SNR84 overexpression on baker's yeast which was exposed to high-temperature, high-sucrose and freeze-thaw stresses. These results suggest that overexpression of the SNR84 gene conferred tolerance of baker's yeast cells to high-temperature, high-sucrose and freeze-thaw stresses and enhanced their leavening ability in high-sucrose and freeze-thaw dough. These findings could provide a valuable insight for breeding of novel stress-resistant baker's yeast strains that are useful for baking.

Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae

The industrial yeast Saccharomyces cerevisiae is a traditional ethanologenic agent and a promising biocatalyst for advanced biofuels production using lignocellulose materials. Here we present the genomic background of type strain NRRL Y-12632 and its transcriptomic response to 5-hydroxymethyl-2-furaldehyde (HMF), a commonly encountered toxic compound liberated from lignocellulosic-biomass pretreatment, in dissecting the genomic mechanisms of yeast tolerance. Compared with the genome of laboratory model strain S288C, we identified more than 32,000 SNPs in Y-12632 with 23,000 missense and nonsense SNPs. Enriched sequence mutations occurred for genes involved in MAPK- and phosphatidylinositol (PI)- signaling pathways in strain Y-12632, with 41 and 13 genes containing non-synonymous SNPs, respectively. Many of these mutated genes displayed consistent up-regulated signature expressions in response to challenges of 30 mM HMF. Analogous single-gene deletion mutations of these genes showed significantly sensitive growth response on a synthetic medium containing 20 mM HMF. Our results suggest at least three MAPK-signaling pathways, especially for the cell-wall integrity pathway, and PI-signaling pathways to be involved in mediation of yeast tolerance against HMF in industrial yeast Saccharomyces cerevisiae. Higher levels of sequence variations were also observed for genes involved in purine and pyrimidine metabolism pathways.

Enhanced freeze tolerance of baker’s yeast by overexpressed trehalose-6-phosphate synthase gene (TPS1) and deleted trehalase genes in frozen dough

Several recombinant strains with overexpressed trehalose-6-phosphate synthase gene (TPS1) and/or deleted trehalase genes were obtained to elucidate the relationships between TPS1, trehalase genes, content of intracellular trehalose and freeze tolerance of baker’s yeast, as well as improve the fermentation properties of lean dough after freezing. In this study, strain TL301TPS1 overexpressing TPS1 showed 62.92 % higher trehalose-6-phosphate synthase (Tps1) activity and enhanced the content of intracellular trehalose than the parental strain. Deleting ATH1 exerted a significant effect on trehalase activities and the degradation amount of intracellular trehalose during the first 30 min of prefermentation. This finding indicates that acid trehalase (Ath1) plays a role in intracellular trehalose degradation. NTH2 encodes a functional neutral trehalase (Nth2) that was significantly involved in intracellular trehalose degradation in the absence of the NTH1 and/or ATH1 gene. The survival ratio, freeze-tolerance ratio and relative fermentation ability of strain TL301TPS1 were approximately twice as high as those of the parental strain (BY6-9α). The increase in freeze tolerance of strain TL301TPS1 was accompanied by relatively low trehalase activity, high Tps1 activity and high residual content of intracellular trehalose. Our results suggest that overexpressing TPS1 and deleting trehalase genes are sufficient to improve the freeze tolerance of baker’s yeast in frozen dough. The present study provides guidance for the commercial baking industry as well as the research on the intracellular trehalose mobilization and freeze tolerance of baker’s yeast.