Stress tolerance phenotype of industrial yeast: industrial cases, cellular changes, and improvement strategies

Metabolomic insights into the effect of chickpea protein hydrolysate on the freeze-thaw tolerance of industrial yeasts

The use of frozen dough is an intensive food-processing practice that contributes to the development of chain operations in the bakery industry. However, the fermentation activity of yeasts in frozen dough can be severely damaged by freeze-thaw stress, thereby degrading the final bread quality. In this study, chickpea protein hydrolysate significantly improved the quality of steamed bread made from frozen dough while enhancing the yeast survival rate and maintaining yeast cell structural integrity under freeze-thaw stress. The mechanism underlying this protective role of chickpea protein hydrolysate was further investigated by untargeted metabolomics analysis, which suggested that chickpea protein hydrolysate altered the intracellular metabolites associated with central carbon metabolism, amino acid synthesis, and lipid metabolism to improve yeast cell freeze-thaw tolerance. Therefore, chickpea protein hydrolysate is a promising natural antifreeze component for yeast cryopreservation in the frozen dough industry.

Effect of different stress conditions on the formation of amino acid derivatives by Brewer's and Baker's yeast during fermentation

The effects of environmental stresses on the formation of amino acid derivatives by Saccharomyces cerevisiae NCYC 88 and Saccharomyces cerevisiae NCYC 79 were investigated. Fermentation was performed in model systems under different temperature, pH, alcohol, phenolic, and osmotic stress conditions, as well as in beer and dough. According to stress response molecules, yeasts were more affected by osmotic, temperature, and alcohol stresses. Both yeast strains increased the formation of kynurenic acid, tryptophan ethyl ester, tryptophol, and gamma-aminobutyric acid under osmotic stress conditions in model systems. Indole-3-acetic acid was found to be higher in the ferulic acid stress dough (262 µg/kg dry weight, d.w.) compared to the control dough (132 µg/kg d.w.) at the end of the fermentation. The results may enable the development of new strategies for designing novel foods with a desired composition of bioactive amino acid derivatives.

Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae

Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6Δ) is the most sensitive to CA. Based on the omics analysis of ERG6Δ under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP+ were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6Δ. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.

Unveiling the super tolerance of Candida nivariensis to oxidative stress: insights into the involvement of a catalase

Yeast cells involved in fermentation processes face various stressors that disrupt redox homeostasis and cause cellular damage, making the study of oxidative stress mechanisms crucial. In this investigation, we isolated a resilient yeast strain, Candida nivariensis GXAS-CN, capable of thriving in the presence of high concentrations of H2O2. Transcriptomic analysis revealed the up-regulation of multiple antioxidant genes in response to oxidative stress. Deletion of the catalase gene Cncat significantly impacted H2O2-induced oxidative stress. Enzymatic analysis of recombinant CnCat highlighted its highly efficient catalase activity and its essential role in mitigating H2O2. Furthermore, over-expression of CnCat in Saccharomyces cerevisiae improved oxidative resistance by reducing intracellular ROS accumulation. The presence of multiple stress-responsive transcription factor binding sites at the promoters of antioxidative genes indicates their regulation by different transcription factors. These findings demonstrate the potential of utilizing the remarkably tolerant C. nivariensis GXAS-CN or enhancing the resistance of S. cerevisiae to improve the efficiency and cost-effectiveness of industrial fermentation processes.IMPORTANCEEnduring oxidative stress is a crucial trait for fermentation strains. The importance of this research is its capacity to advance industrial fermentation processes. Through an in-depth examination of the mechanisms behind the remarkable H2O2 resistance in Candida nivariensis GXAS-CN and the successful genetic manipulation of this strain, we open the door to harnessing the potential of the catalase CnCat for enhancing the oxidative stress resistance and performance of yeast strains. This pioneering achievement creates avenues for fine-tuning yeast strains for precise industrial applications, ultimately leading to more efficient and cost-effective biotechnological processes.

An Evolved Strain of the Oleaginous Yeast Rhodotorula toruloides, Multi-Tolerant to the Major Inhibitors Present in Lignocellulosic Hydrolysates, Exhibits an Altered Cell Envelope

The presence of toxic compounds in lignocellulosic hydrolysates (LCH) is among the main barriers affecting the efficiency of lignocellulose-based fermentation processes, in particular, to produce biofuels, hindering the production of intracellular lipids by oleaginous yeasts. These microbial oils are promising sustainable alternatives to vegetable oils for biodiesel production. In this study, we explored adaptive laboratory evolution (ALE), under methanol- and high glycerol concentration-induced selective pressures, to improve the robustness of a Rhodotorula toruloides strain, previously selected to produce lipids from sugar beet hydrolysates by completely using the major C (carbon) sources present. An evolved strain, multi-tolerant not only to methanol but to four major inhibitors present in LCH (acetic acid, formic acid, hydroxymethylfurfural, and furfural) was isolated and the mechanisms underlying such multi-tolerance were examined, at the cellular envelope level. Results indicate that the evolved multi-tolerant strain has a cell wall that is less susceptible to zymolyase and a decreased permeability, based on the propidium iodide fluorescent probe, in the absence or presence of those inhibitors. The improved performance of this multi-tolerant strain for lipid production from a synthetic lignocellulosic hydrolysate medium, supplemented with those inhibitors, was confirmed.

Food yeasts: occurrence, functions, and stress tolerance in the brewing of fermented foods

With the rapid development of systems biology technology, there is a deeper understanding of the molecular biological mechanisms and physiological characteristics of microorganisms. Yeasts are widely used in the food industry with their excellent fermentation performances. While due to the complex environments of food production, yeasts have to suffer from various stress factors. Thus, elucidating the stress mechanisms of food yeasts and proposing potential strategies to improve tolerance have been widely concerned. This review summarized the recent signs of progress in the variety, functions, and stress tolerance of food yeasts. Firstly, the main food yeasts occurred in fermented foods, and the taxonomy levels are demonstrated. Then, the main functions of yeasts including aroma enhancer, safety performance enhancer, and fermentation period reducer are discussed. Finally, the stress response mechanisms of yeasts and the strategies to improve the stress tolerance of cells are reviewed. Based on sorting out these related recent researches systematically, we hope that this review can provide help and approaches to further exert the functions of food yeasts and improve food production efficiency.

Dung beetle-associated yeasts display multiple stress tolerance: a desirable trait of potential industrial strains

BACKGROUND

Stress-tolerant yeasts are highly desirable for cost-effective bioprocessing. Several strategies have been documented to develop robust yeasts, such as genetic and metabolic engineering, artificial selection, and natural selection strategies, among others. However, the significant drawbacks of such techniques have motivated the exploration of naturally occurring stress-tolerant yeasts. We previously explored the biodiversity of non-conventional dung beetle-associated yeasts from extremophilic and pristine environments in Botswana (Nwaefuna AE et.al., Yeast, 2023). Here, we assessed their tolerance to industrially relevant stressors individually, such as elevated concentrations of osmolytes, organic acids, ethanol, and oxidizing agents, as well as elevated temperatures.

RESULTS

Our findings suggest that these dung beetle-associated yeasts tolerate various stresses comparable to those of the robust bioethanol yeast strain, Saccharomyces cerevisiae (Ethanol Red™). Fifty-six percent of the yeast isolates were tolerant of temperatures up to 42 °C, 12.4% of them could tolerate ethanol concentrations up to 9% (v/v), 43.2% of them were tolerant to formic acid concentrations up to 20 mM, 22.7% were tolerant to acetic acid concentrations up to 45 mM, 34.0% of them could tolerate hydrogen peroxide up to 7 mM, and 44.3% of the yeasts could tolerate osmotic stress up to 1.5 M.

CONCLUSION

The ability to tolerate multiple stresses is a desirable trait in the selection of novel production strains for diverse biotechnological applications, such as bioethanol production. Our study shows that the exploration of natural diversity in the search for stress-tolerant yeasts is an appealing approach for the development of robust yeasts.

Engineering acetyl-CoA metabolism to enhance stress tolerance of yeast by regulating membrane functionality

Zygosaccharomyces rouxii has excellent fermentation performance and good tolerance to osmotic stress. Acetyl-CoA is a crucial intermediate precursor in the central carbon metabolic pathway of yeast. This study investigated the effect of engineering acetyl-CoA metabolism on the membrane functionality and stress tolerance of yeast. Firstly, exogenous supplementation of acetyl-CoA improved the biomass and the ability of unsaturated fatty acid synthesis of Z. rouxii under salt stress. Q-PCR results suggested that the gene ACSS (coding acetyl-CoA synthetase) was significantly up-expressed. Subsequently, the gene ACSS from Z. rouxii was transformed and heterologously expressed in S. cerevisiae. The recombinant cells exhibited better multiple stress (salt, acid, heat, and cold) tolerance, higher fatty acid contents, membrane integrity, and fluidity. Our findings may provide a suitable means to enhance the stress tolerance and fermentation efficiency of yeast under harsh fermentation environments.

Peptide extract from spent yeast improves resistance of Saccharomyces cerevisiae to oxidative stress

Yeast cells face various stress factors during industrial fermentations, since they are exposed to harsh environmental conditions, which may impair biomolecules productivity and yield. In this work, the use of an antioxidant peptide extract obtained from industrial spent yeast was explored as supplement for Saccharomyces cerevisiae fermentation to prevent a common bottleneck: oxidative stress. For that, a recombinant yeast strain, producer of β-farnesene, was firstly incubated with 0.5 and 0.7 g/L peptide extract, in the presence and absence of hydrogen peroxide (an oxidative stress inducer), for 1-5 h, and then assayed for intracellular reactive oxygen species, and growth ability in agar spot assays. Results showed that under 2 mM H₂O_2, the peptide extract could improve cells growth and reduce reactive oxygen species production. Therefore, this antioxidant effect was further evaluated in shake-flasks and 2-L bioreactor batch fermentations. Peptide extract (0.7 g/L) was able to increase yeast resistance to the oxidative stress promoted by 2 mM H₂O₂, by reducing reactive oxygen species levels between 1.2- and 1.7-fold in bioreactor and between 1.2- and 3-fold in shake-flask fermentations. Moreover, improvements on yeast cell density of up to 1.5-fold and 2-fold, and on biomolecule concentration of up to 1.6-fold and 2.8-fold, in bioreactor and shake-flasks, respectively, were obtained. Thus, culture medium supplementation with antioxidant peptide extracted from industrial spent yeast is a promising strategy to improve fermentation performance while valuing biomass waste. This valorization can promote a sustainable and eco-friendly solution for the biotechnology industry by the implementation of a circular economy model. KEY POINTS: • Peptide extract from spent yeast applied for the first time on yeast fermentation. • Antioxidant peptide extract enhanced S. cerevisiae oxidative stress resistance. • Fermentation performance under stress improved by peptide extract supplementation.

Fluorescence lifetime imaging of NAD(P)H upon oxidative stress in Kluyveromyces marxianus

K. marxianus is a promising cell factory for producing heterologous proteins. Oxidative stresses were raised during overexpression of heterologous proteins, leading to the shift of the redox state. How to measure the redox state of live K. marxianus cells without perturbing their growth remains a big challenge. Here, a fluorescence lifetime imaging (FLIM)-based method was developed in live K. marxianus cells. During the early exponential growth, K. marxianus cells exhibited an increased mean fluorescence lifetime (τ-mean) of NAD(P)H compared with Saccharomyces cerevisiae cells, which was consistent with the preference for respiration in K. marxianus cells and that for fermentation in S. cerevisiae cells. Upon oxidative stresses induced by high temperature or H2O2, K. marxianus cells exhibited an increased τ-mean in company with decreased intracellular NAD(P)H/NAD(P)+, suggesting a correlation between an increased τ-mean and a more oxidized redox state. The relationship between τ-mean and the expression level of a heterologous protein was investigated. There was no difference between the τ-means of K. marxianus strains which were not producing a heterologous protein. The τ-mean of a strain yielding a high level of a heterologous protein was higher than that of a low-yielding strain. The results suggested the potential application of FLIM in the non-invasive screen of high-yielding cells.

Proteomics Readjustment of the Yarrowia lipolytica Yeast in Response to Increased Temperature and Alkaline Stress

Yeasts cope with a wide range of environmental challenges using different adaptive mechanisms. They can prosper at extreme ambient pH and high temperatures; however, their adaptation mechanisms have not been entirely investigated. Previously, we showed the pivotal role and flexibility of the sugar and lipid composition of Yarrowia lipolytica W 29 upon adaptation to unfavorable conditions. In this study, we showed that extreme pH provoked significant changes in the cell wall proteins expression, with an increase in both the chaperones of heat shock protein HSP60 and some other proteins with chaperone functions. The mitochondria activity changes inducing the VDAC and malate dehydrogenase played an essential role in the adaptation, as did the altered carbohydrate metabolism, promoting its shift towards the pyruvate formation rather than gluconeogenesis. The elevated temperature led to changes in the cell wall proteins and chaperones, the induced expression of the proteins involved in the cell structural organization, ribosomal proteins, and the enzymes of formaldehyde degradation. Moreover, the readjustment of the protein composition and amount under combined stress indicated the promotion of catabolic processes related to scavenging the damaged proteins and lipids. Under all of the stress conditions studied, the process of folding, stress resistance, redox adaptation, and oxidative phosphorylation were the dominant pathways. The combined chronic alkaline and heat stress (pH 9.0, 38 °C) led to cross-adaptation, which caused "switching" over the traditional metabolism to the adaptation to the most damaging stress factor, namely the increased temperature.

Conferring thermotolerant phenotype to wild-type Yarrowia lipolytica improves cell growth and erythritol production

In microbial engineering, heat stress is an important environmental factor modulating cell growth, metabolic flux distribution and the synthesis of target products. Yarrowia lipolytica, as a GARS (generally recognized as safe) nonconventional yeast, has been widely used in the food industry, especially as the host of erythritol production. Biomanufacturing economics is limited by the high operational cost of cooling energy in large-scale fermentation. It is of great significance to select thermotolerant Y. lipolytica to reduce the cooling cost and elucidate the heat-resistant mechanism at molecular level. For this purpose, we performed adaptive evolution and obtained a thermotolerant strain named Y. lipolytica BBE-18. Transcriptome analysis allows us to identify four genes in thiamine metabolism pathway that are responsible for the complicated thermotolerant phenotype. The heat-resistant phenotype was validated with the model strain Y. lipolytica Po1f by overexpression of single and combined genes. Then, conferring the thermotolerant phenotype to the wild-type Y. lipolytica BBE-17 enable the strain to produce three-times more erythritol of the control strain with 3°C higher than optimal cultivation temperature. To our knowledge, this is the first report on engineering heat-resistant phenotype to improve the erythritol production in Y. lipolytica. However, due to the increase of culture temperature, a large amount of adenosine triphosphate is consumed to ensure the life activities of Y. lipolytica which limits the potential of cell synthetic products to a certain extent. Even so, this study provides a reference for Y. lipolytica to produce other products under high temperature.

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.

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.

Superoxide dismutase: an updated review on its health benefits and industrial applications

Many short-lived and highly reactive oxygen species, such as superoxide anion (O₂^-) and hydrogen peroxide (H₂O₂), are toxic or can create oxidative stress in cells, a response involved in the pathogenesis of numerous diseases depending on their concentration, location, and cellular conditions. Superoxide dismutase (SOD) activities as an endogenous and exogenous cell defense mechanism include the potential use in treating various diseases, improving the potential use in treating various diseases, and improving food-stuffs preparation dietary supplements human nutrition. Published work indicates that SOD regulates oxidative stress, lipid metabolism, inflammation, and oxidation in cells. It can prevent lipid peroxidation, the oxidation of low-density lipoprotein in macrophages, lipid droplets' formation, and the adhesion of inflammatory cells into endothelial monolayers. It also expresses antioxidant effects in numerous cancer-related processes. Additionally, different forms of SOD may also augment food processing and pharmaceutical applications, exhibit anticancer, antioxidant, and anti-inflammatory effects, and prevent arterial problems by protecting the proliferation of vascular smooth muscle cells. Many investigations in this review have reported the therapeutic ability and physiological importance of SOD. Because of their antioxidative effects, SODs are of great potential in the medicinal, cosmetic, food, farming and chemical industries. This review discusses the findings of human and animal studies that support the advantages of SOD enzyme regulations to reduce the formation of oxidative stress in various ways.

Yeast Fermentation at Low Temperatures: Adaptation to Changing Environmental Conditions and Formation of Volatile Compounds

Yeast plays a key role in the production of fermented foods and beverages, such as bread, wine, and other alcoholic beverages. They are able to produce and release from the fermentation environment large numbers of volatile organic compounds (VOCs). This is the reason for the great interest in the possibility of adapting these microorganisms to fermentation at reduced temperatures. By doing this, it would be possible to obtain better sensory profiles of the final products. It can reduce the addition of artificial flavors and enhancements to food products and influence other important factors of fermented food production. Here, we reviewed the genetic and physiological mechanisms by which yeasts adapt to low temperatures. Next, we discussed the importance of VOCs for the food industry, their biosynthesis, and the most common volatiles in fermented foods and described the beneficial impact of decreased temperature as a factor that contributes to improving the composition of the sensory profiles of fermented foods.

Importance of Downstream Processing of Natural Astaxanthin for Pharmaceutical Application

Astaxanthin (ASX) is a xanthophyll pigment considered as a nutraceutical with high antioxidant activity. Several clinical trials have shown the multiple health benefits of this molecule; therefore, it has various pharmaceutical industry applications. Commercial astaxanthin can be produced by chemical synthesis or through biosynthesis within different microorganisms. The molecule produced by the microorganisms is highly preferred due to its zero toxicity and superior therapeutic properties. However, the biotechnological production of the xanthophyll is not competitive against the chemical synthesis, since the downstream process may represent 70–80% of the process production cost. These operations denote then an opportunity to optimize the process and make this alternative more competitive. Since ASX is produced intracellularly by the microorganisms, high investment and high operational costs, like centrifugation and bead milling or high-pressure homogenization, are mainly used. In cell recovery, flocculation and flotation may represent low energy demanding techniques, whereas, after cell disruption, an efficient extraction technique is necessary to extract the highest percentage of ASX produced by the cell. Solvent extraction is the traditional method, but large-scale ASX production has adopted supercritical CO2 (SC-CO2), an efficient and environmentally friendly technology. On the other hand, assisted technologies are extensively reported since the cell disruption, and ASX extraction can be carried out in a single step. Because a high-purity product is required in pharmaceuticals and nutraceutical applications, the use of chromatography is necessary for the downstream process. Traditionally liquid-solid chromatography techniques are applied; however, the recent emergence of liquid-liquid chromatography like high-speed countercurrent chromatography (HSCCC) coupled with liquid-solid chromatography allows high productivity and purity up to 99% of ASX. Additionally, the use of SC-CO2, coupled with two-dimensional chromatography, is very promising. Finally, the purified ASX needs to be formulated to ensure its stability and bioavailability; thus, encapsulation is widely employed. In this review, we focus on the processes of cell recovery, cell disruption, drying, extraction, purification, and formulation of ASX mainly produced in Haematococcus pluvialis, Phaffia rhodozyma, and Paracoccus carotinifaciens. We discuss the current technologies that are being developed to make downstream operations more efficient and competitive in the biotechnological production process of this carotenoid.

Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation

The continuous usage of single Saccharomyces cerevisiae strains as starter cultures in fermentation led to the domestication and propagation of highly specialized strains in fermentation, resulting in the standardization of wines and beers. In this way, hundreds of commercial strains have been developed to satisfy producers’ and consumers’ demands, including beverages with high/low ethanol content, nutrient deprivation tolerance, diverse aromatic profiles, and fast fermentations. However, studies in the last 20 years have demonstrated that the genetic and phenotypic diversity in commercial S. cerevisiae strains is low. This lack of diversity limits alternative wines and beers, stressing the need to explore new genetic resources to differentiate each fermentation product. In this sense, wild strains harbor a higher than thought genetic and phenotypic diversity, representing a feasible option to generate new fermentative beverages. Numerous recent studies have identified alleles in wild strains that could favor phenotypes of interest, such as nitrogen consumption, tolerance to cold or high temperatures, and the production of metabolites, such as glycerol and aroma compounds. Here, we review the recent literature on the use of commercial and wild S. cerevisiae strains in wine and beer fermentation, providing molecular evidence of the advantages of using wild strains for the generation of improved genetic stocks for the industry according to the product style.