Isolation of baker's yeast mutants with proline accumulation that showed enhanced tolerance to baking-associated stresses

Improvement of the freezing resistance characteristics of yeast in dough starter

Improving the freezing resistance of yeast in dough starters is one of the most effective methods to promote the healthy development of frozen dough technology. When the dough starter was composed of yeast, lactic acid bacteria and acetic acid bacteria, the microbial proportion was 10:1:5, and the ratio of wheat flour to corn flour was 1:1. The proline contents of the starters and the survival rates and fermentation capacity of yeast significantly increased compared with those of the starter composed of yeast and wheat flour only (P < 0.05). Laser confocal microscopy observation showed that the cell membrane damage of yeast obviously decreased. Low-field nuclear magnetic resonance method revealed that the water distribution state of starters changed. Adding corn flour and acetic acid bacteria to dough starter in appropriate proportions improves yeast freezing resistance.

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.

Fermentation properties and functional stability of dough starter Jiaozi and Laomian after frozen storage

Purpose

This study aims to investigate the effects of frozen storage on the stability of traditional dough starters in China.

Methods

The microbial community structure and abundance of related metabolic genes in different fermented sourdough prepared by Jiaozi (JZ) and Laomian (LM) starters before and after frozen storage at -20°C for half a year were analyzed using the shotgun metagenomic sequencing method, and differences in characteristics of texture in steamed bread were also compared by formal methods.

Results

The fermentation ability (FA) and metabolic activities of yeast in the JZH sourdough (started by JZ which was stored at -20°C for half a year) were better than those of LMH sourdough (started by LM which was stored at -20°C for half a year). The dominant genera of Acetobacter were found to be increased in the JZH0 sourdough (started by JZH and fermented for 0 h) and those of Lactobacillus were found to be decreased. Lactobacillus (98.72%), Pediococcus (0.37%), Saccharomyces (0.27%), and Acetobacter (0.01%), were dominant in sourdough LMH0 (started by LMH and fermented for 0 h). The abundances of "oxidative phosphorylation-related enzymes" and the "biosynthesis of glutamate"-related enzymes and genes related to "biosynthesis of glutamate" and "unsaturated fatty acid" were higher in JZH0 than in the JZ0 sourdough (started by JZ without being frozen and fermented for 0 h). The good FA of yeast, the acid production capacity of bacteria in the sourdough, and the quality of the JZH steamed bread (made by the JZH starter) indicated the better freezing tolerance of the microorganisms in JZ than in LM.

Conclusion

The conclusion of this study suggests the better application potential of the JZ as the fermentation starter in actual production.

Metabolomics analysis of freeze-thaw tolerance enhancement mechanism of ε-poly-l-lysine on industrial yeast

Antimicrobial polycationic peptide ε-poly-l-lysine (ε-PL) enhanced the freeze-thaw tolerance of industrial yeast; the enhancement mechanism of ε-PL on yeast was studied. Results showed that a ε-PL coating was observed in ε-PL-treated yeast. After 4 times of freeze-thaw, the cell viability, glycerol content, and CO₂ production of 0.6 mg/mL ε-PL-treated yeast were higher than those of untreated yeast, specifically, the cell viability of ε-PL-treated yeast was 87.6%, and that of untreated yeast was 68.5%. Metabolomic results showed that the enhancement mechanism of ε-PL on yeast was related to the promotion of cell membrane-related fatty acid synthesis pathways before freeze-thaw treatment, and the promotion of trehalose biosynthesis and glycerophospholipid metabolism pathways after freeze-thaw. Furthermore, ε-PL induced inhibition of the tricarboxylic acid cycle, resulting in a longer stationary phase at the beginning of the freeze-thaw and ultimately providing a higher level of freeze-thaw stress tolerance than untreated yeast.

Role of Gln79 in Feedback Inhibition of the Yeast γ-Glutamyl Kinase by Proline

Awamori, the traditional distilled alcoholic beverage of Okinawa, Japan, is brewed with the yeast Saccharomyces cerevisiae. During the distillation process after the fermentation, enormous quantities of distillation residues containing yeast cells must be disposed of, and this has recently been recognized as a major problem both environmentally and economically. Proline, a multifunctional amino acid, has the highest water retention capacity among amino acids. Therefore, distillation residues with large amounts of proline could be useful in cosmetics. Here, we isolated a yeast mutant with high levels of intracellular proline and found a missense mutation (Gln79His) on the PRO1 gene encoding the γ-glutamyl kinase Pro1, a limiting enzyme in proline biosynthesis. The amino acid change of Gln79 to His in Pro1 resulted in desensitization to the proline-mediated feedback inhibition of GK activity, leading to the accumulation of proline in cells. Biochemical and in silico analyses showed that the amino acid residue at position 79 is involved in the stabilization of the proline binding pocket in Pro1 via a hydrogen-bonding network, which plays an important role in feedback inhibition. Our current study, therefore, proposed a possible mechanism underlying the feedback inhibition of γ-glutamyl kinase activity. This mechanism can be applied to construct proline-accumulating yeast strains to effectively utilize distillation residues.

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.

Overcoming bread quality decay concerns: main issues for bread shelf life as a function of biological leavening agents and different extra ingredients used in formulation. A review

As is widely accepted, the quality decay of freshly baked bread that affects product shelf life is the result of a complex multifactorial process that involves physical staling, together with microbiological, chemical and sensorial spoilage. In this context, this paper provides a critical review of the recent literature about the main factors affecting shelf life of bread during post-baking. An overview of the recent findings about the mechanism of bread staling is firstly provided. Afterwards, the effect on staling induced by baker's yeasts and sourdough as well as by the extra ingredients commonly utilized for bread fortification is also addressed and discussed. As inclusion/exclusion criteria, only papers dealing with wheat bread and not with long-life bread or gluten-free bakery products are taken into consideration. Despite recent developments in international scientific literature, the whole mechanism that induces bread staling is far from being completely understood and the best analytical methods to be adopted to measure and/or describe in depth this process appear still debated. In this topic, the effects induced on bread shelf life by the use of biological leavening agents (baker's yeasts and sourdough) as well as by some extra ingredients included in the bread recipe have been individuated as two key issues to be addressed and discussed in terms of their influence on the kinetics of bread staling. © 2020 Society of Chemical Industry.

Effect of overexpression of SNF1 on the transcriptional and metabolic landscape of baker's yeast under freezing stress

Background

Freezing stress is the key factor that affecting the cell activity and fermentation performance of baker’s yeast in frozen dough production. Generally, cells protect themselves from injury and maintain metabolism by regulating gene expression and modulating metabolic patterns in stresses. The Snf1 protein kinase is an important regulator of yeast in response to stresses. In this study, we aim to study the role of the catalytic subunit of Snf1 protein kinase in the cell tolerance and dough leavening ability of baker’s yeast during freezing. Furthermore, the effects of SNF1 overexpression on the global gene expression and metabolite profile of baker’s yeast before and after freezing were analysed using RNA-sequencing and untargeted UPLC − QTOF-MS/MS, respectively.

Results

The results suggest that overexpression of SNF1 was effective in enhancing the cell tolerance and fermentation capacity of baker’s yeast in freezing, which may be related to the upregulated proteasome, altered metabolism of carbon sources and protectant molecules, and changed cell membrane components. SNF1 overexpression altered the level of leucin, proline, serine, isoleucine, arginine, homocitrulline, glycerol, palmitic acid, lysophosphatidylcholine (LysoPC), and lysophosphatidylethanolamine (LysoPE) before freezing, conferring cells resistance in freezing. After freezing, relative high level of proline, lysine, and glycerol maintained by SNF1 overexpression with increased content of LysoPC and LysoPE.

Conclusions

This study will increase the knowledge of the cellular response of baker’s yeast cells to freezing and provide new opportunities for the breeding of low-temperature resistant strains.

History and Domestication of Saccharomyces cerevisiae in Bread Baking

The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.

Frozen-dough baking potential of psychrotolerant Saccharomyces species and derived hybrids

Despite Saccharomyces cerevisiae being a synonym for baker's yeast, the species does not perform well in all baking-related conditions. In particular, dough fermentation, or proofing, is compromised by the species' sensitivity to the low and freezing temperatures that are often used in modern bakeries. Here, screening trials that included representatives of all known Saccharomyces species, showed that S. cerevisiae was generally the most sensitive member of the genus with respect to cold and freezing conditions. We hypothesized therefore that the superior cold tolerance of the non-S. cerevisiae yeast would enable their use as frozen-dough baking strains. To test this, the different yeast species were incorporated into doughs, flash frozen and kept in a frozen state for 14 days. During the proofing stage, dough development was lower in doughs that had been frozen, relative to fresh doughs. This reduction in fermentation performance was however most pronounced with S. cerevisiae. The psychrotolerant yeasts S. eubayanus, S. jurei and S. arboricola showed a strong capacity for post-freeze proofing in terms of dough development and duration of lag phase prior to fermentation. The superior proofing power of these species resulted in breads that were significantly softer and less dense than those prepared with S. cerevisiae. A sensory panel could distinguish the S. cerevisiae and non-S. cerevisiae breads based on their physical properties, but aroma and taste were unaffected by the species employed. To further improve frozen dough baking properties, S. eubayanus, S. jurei and S. arboricola were crossed with baker's yeast through rare mating, and hybrids with improved proofing capacities in both fresh and frozen doughs relative to the parents were created. The use of S. jurei and S. arboricola in baking represents the first potential technological application of these species.

High-level production of ornithine by expression of the feedback inhibition-insensitive N-acetyl glutamate kinase in the sake yeast Saccharomyces cerevisiae

We previously reported that intracellular proline (Pro) confers tolerance to ethanol on the yeast Saccharomyces cerevisiae. In this study, to improve the ethanol productivity of sake, a traditional Japanese alcoholic beverage, we successfully isolated several Pro-accumulating mutants derived from diploid sake yeast of S. cerevisiae by a conventional mutagenesis. Interestingly, one of them (strain A902-4) produced more than 10-fold greater amounts of ornithine (Orn) and Pro compared to the parent strain (K901). Orn is a non-proteinogenic amino acid and a precursor of both arginine (Arg) and Pro. It has some physiological functions, such as amelioration of negative states such as lassitude and improvement of sleep quality. We also identified a homo-allelic mutation in the ARG5,6 gene encoding the Thr340Ile variant N-acetylglutamate kinase (NAGK) in strain A902-4. The NAGK activity of the Thr340Ile variant was extremely insensitive to feedback inhibition by Arg, leading to intracellular Orn accumulation. This is the first report of the removal of feedback inhibition of NAGK activity in the industrial yeast, leading to high levels of intracellular Orn. Moreover, sake and sake cake brewed with strain A902-4 contained 4-5 times more Orn than those brewed with strain K901. The approach described here could be a practical method for the development of industrial yeast strains with overproduction of Orn.

Ice-binding proteins: a remarkable ice crystal regulator for frozen foods

Ice crystal growth during cold storage presents a quality problem in frozen foods. The development of appropriate technical conditions and ingredient formulations is an effective method for frozen food manufacturers to inhibit ice crystals generated during storage and distribution. Ice-binding proteins (IBPs) have great application potential as ice crystal growth inhibitors. The ability of IBPs to retard the growth of ice crystals suggests that IBPs can be used as a natural ice conditioner for a variety of frozen products. In this review, we first discussed the damage caused by ice crystals in frozen foods during freezing and frozen storage. Next, the methods and technologies for production, purification and evaluation of IBPs were summarized. Importantly, the present review focused on the characteristics, structural diversity and mechanisms of IBPs, and the application advances of IBPs in food industry. Finally, the challenges and future perspectives of IBPs are also discussed. This review may provide a better understanding of IBPs and their applications in frozen products, providing some valuable information for further research and application of IBPs.

Proline Homeostasis in Saccharomyces cerevisiae: How Does the Stress-Responsive Transcription Factor Msn2 Play a Role?

Overexpression of MSN2, which is the transcription factor gene in response to stress, is well-known to increase the tolerance of the yeast Saccharomyces cerevisiae cells to a wide variety of environmental stresses. Recent studies have found that the Msn2 is a feasible potential mediator of proline homeostasis in yeast. This result is based on the finding that overexpression of the MSN2 gene exacerbates the cytotoxicity of yeast to various amino acid analogs whose uptake is increased by the active amino acid permeases localized on the plasma membrane as a result of a dysfunctional deubiquitination process. Increased understanding of the cellular responses induced by the Msn2-mediated proline incorporation will provide better comprehension of how cells respond to and counteract to different kinds of stimuli and will also contribute to the breeding of industrial yeast strains with increased productivity.

Transcriptome analysis reveals the protection mechanism of proanthocyanidins for Saccharomyces cerevisiae during wine fermentation

Grape-derived proanthocyanidins could act as a protector against various environmental stresses for Saccharomyces cerevisiae during wine fermentation, resulting in the increased physiological activity, fermentation efficiency and improved wine quality. In order to explore the possible protection mechanism of proanthocyanidins globally, RNA-seq analysis for wine yeast AWRI R2 cultivated with 0 g/L (group A), 0.1 g/L (group B), 1.0 g/L (group C) proanthocyanidins were applied in this study. Differentially expressed genes were enriched into six metabolic pathways including vitamin B₆, thiamine, amino acids, aminoacyl-tRNA, carbohydrate and steroid based on KEGG enrichment analysis. Four key genes (SNZ2, THI6, THI21 and THI80), participated in the biosynthesis of vitamin B₆ and thiamine, were up-regulated significantly in proanthocyanidins treated yeast cells and the gene expression levels were verified by RT-qPCR. Yeast cells supplemented with proanthocyanidins performed increased intracellular levels of vitamin B₆ and thiamine and higher cell viability compared to the control group. In addition, the composition of intracellular fatty acids showed an obvious alternation in proanthocyanidins-treated yeast cells, in which the UFAs content increased whereas the SFA content decreased. In general, we provided an indirect protection effect of proanthocyanidins on the yeast cells to alleviate environmental stresses during wine fermentation.

Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae

In many plants and microorganisms, intracellular proline has a protective role against various stresses, including heat-shock, oxidation and osmolarity. Environmental stresses induce cellular senescence in a variety of eukaryotes. Here we showed that intracellular proline regulates the replicative lifespan in the budding yeast Saccharomyces cerevisiae. Deletion of the proline oxidase gene PUT1 and expression of the γ-glutamate kinase mutant gene PRO1-I150T that is less sensitive to feedback inhibition accumulated proline and extended the replicative lifespan of yeast cells. Inversely, disruption of the proline biosynthetic genes PRO1, PRO2, and CAR2 decreased stationary proline level and shortened the lifespan of yeast cells. Quadruple disruption of the proline transporter genes unexpectedly did not change intracellular proline levels and replicative lifespan. Overexpression of the stress-responsive transcription activator gene MSN2 reduced intracellular proline levels by inducing the expression of PUT1, resulting in a short lifespan. Thus, the intracellular proline levels at stationary phase was positively correlated with the replicative lifespan. Furthermore, multivariate analysis of amino acids in yeast mutants deficient in proline metabolism showed characteristic metabolic profiles coincident with longevity: acidic and basic amino acids and branched-chain amino acids positively contributed to the replicative lifespan. These results allude to proline metabolism having a physiological role in maintaining the lifespan of yeast cells.

Involvement of the stress-responsive transcription factor gene MSN2 in the control of amino acid uptake in Saccharomyces cerevisiae

The transcriptional factor Msn2 plays a pivotal role in response to environmental stresses by activating the transcription of stress-responsive genes in Saccharomyces cerevisiae. Our previous studies demonstrate that intracellular proline acts as a key protectant against various stresses. It is unknown, however, whether Msn2 is involved in proline homeostasis in S. cerevisiae cells. We here found that MSN2-overexpressing (MSN2-OE) cells showed higher sensitivity to a toxic analogue of proline, l-azetidine-2-carboxylic acid (AZC), as well as to the other amino acid toxic analogues, than wild-type cells. Overexpression of MSN2 increased the intracellular content of AZC, suggesting that Msn2 positively regulates the uptake of proline. Among the known proline permease genes, GNP1 was shown to play a predominant role in the AZC toxicity. Based on quantitative real-time PCR and western blot analyses, the overexpression of MSN2 did not induce any increases in the transcript levels of GNP1 or the other proline permease genes, while the amount of the Gnp1 protein was markedly increased in MSN2-OE cells. Microscopic observation suggested that the endocytic degradation of Gnp1 was impaired in MSN2-OE cells. Thus, this study sheds light on a novel link between the Msn2-mediated global stress response and the amino acid homeostasis in S. cerevisiae.

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.

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.

Strategies to Improve Saccharomyces cerevisiae: Technological Advancements and Evolutionary Engineering

Bakery industries are thriving to augment the diverse properties of Saccharomyces cerevisiae to increase its flavor, texture and nutritional parameters to attract the more consumers. The improved technologies adopted for quality improvement of baker's yeast are attracting the attention of industry and it is playing a pivotal role in redesigning the quality parameters. Modern yeast strain improvement tactics revolve around the use of several advanced technologies such as evolutionary engineering, systems biology, metabolic engineering, genome editing. The review mainly deals with the technologies for improving S. cerevisiae, with the objective of broadening the range of its industrial applications.

Genome-wide BigData analytics: Case of yeast stress signature detection

It has been generally recognized that BigData analytics presently have most significant impact on computer inference in life sciences, such as genome wide association studies (GWAS) in basic research and personalized medicine, and its importance will further increase in near future. In this work non-parametric separation of responsive yeast genes from experimental data obtained in chemostat cultivation under dilution rate and nutrient limitations with basic biogenic elements (C,N,S,P), and the specific leucine and uracil auxothropic limitations. Elastic net models are applied for the detection of the key responsive genes for each of the specific limitations. Bootstrap and perturbation methods are used to determine the most important responsive genes and corresponding quantiles applied to the complete data set for all of the nutritional and growth rate limitations. The model predicts that response of gene YOR348C, involved in proline metabolism, as the key signature of stress. Based on literature data, the obtained result are confirmed experimentally by the biochemistry of plants under physical and chemical stress, also by functional genomics of bakers yeast, and also its important function in human tumorogenesis is observed.