Endocytic tethers modulate unconventional GAPDH secretion

Yeast cell walls contain both classically-secreted and unconventionally-secreted proteins. The latter class lacks the signal sequence for translocation into the ER, therefore these proteins are transported to the wall by uncharacterized mechanisms. One such protein is the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) which is abundant in the cytosol, but also found in the yeast cell wall where it is enzymatically active. We screened diploid Saccharomyces cerevisiae homozygous gene deletions for changes in cell wall GAPDH activity. Deletions targeting endocytic tethers in the endolysosomal system had the largest effects on GAPDH secretion, including vps21, bro1, vps41, and pep12. The predominant GAPDH isoform Tdh3 was partially localized to endolysosomal compartments, including multivesicular bodies, which are common entry points to unconventional protein secretion pathways. Yeast lacking the endosomal Rab5-GTPase Vps21 had defects in GAPDH secretion as well as delayed entry into to the endolysosomal compartments. Therefore, we conclude that entry into the endolysosomal compartment facilitates non-conventional secretion of GAPDH.

Impact of Culture Duration on the Properties and Functionality of Yeast-Derived Extracellular Vesicles

Extracellular vesicles (EVs), lipid bilayer nanovesicles secreted by cells, carry nucleic acids, proteins, and other bioactive molecules that influence recipient cells and modulate various biological processes. This study investigated how energy depletion and fermentation processes influence the characteristics and physiological functions of EVs secreted by Saccharomyces cerevisiae. Specifically, we analyzed EVs derived from 24-h cultures, representing the glucose utilization phase, and 72-h cultures, representing the starvation stage. Under energy-depleted conditions (72-h cultures), yeast secreted a higher number of EV particles, albeit with a smaller average particle size. In contrast, EVs from yeast cultured for 24 h, during the glucose utilization phase, were enriched in Pep12-rich endosome-derived vesicles and exhibited 71% higher cellular internalization efficiency. Proteomic and transcriptomic analyses revealed distinct protein and microRNA profiles between EVs from 24- and 72-h cultures, highlighting their potential roles in tissue regeneration, cell proliferation, and collagen synthesis. As a result, EVs derived from 24-h cultures exhibited a 15% greater effect in promoting collagen synthesis. The differential effects on collagen production may be attributed to the efficiency of endocytosis and the specific protein and microRNA cargo of the EVs. This study emphasizes the functional potential and unique properties of yeast-derived EVs while proposing strategies to modulate EV composition by adjusting the yeast culture duration and the energy source in the medium. Further research is needed to control yeast-produced EV components and to understand their mechanisms of action for effective therapeutic applications.

Transcriptional response of Saccharomyces cerevisiae during competition with S. kudriavzevii: Genetic expression variability and accelerated activation

Transcriptomic studies have become an essential tool to understand the response of yeast to stimuli. The present work analyses the reaction of eight Saccharomyces cerevisiae strains with varying competitive abilities against a competitor (CR85, Saccharomyces kudriavzevii) in co-cultured fermentations. RNA sequencing (RNAseq) was performed at three very early time points after strains coinoculation in fermentation to delimit exactly when S. cerevisiae's response is triggered. A rapid response to its competitor, including activation of the glycolytic pathway, ribosomal metabolism, and nucleotide synthesis, is crucial for the dominance of S. cerevisiae strain in mixed fermentations. Additionaly, the study highlights the necessity of investigating individual yeast strains rather than a holistic species view, as significant variations in responses are observed among strains of the same clade.

Evaluation of Biotechnological Active Peptides Secreted by Saccharomyces cerevisiae with Potential Skin Benefits

Biotechnological active peptides are gaining interest in the cosmetics industry due to their antimicrobial, anti-inflammatory, antioxidant, and anti-collagenase (ACE) effects, as well as wound healing properties, making them suitable for cosmetic formulations. The antimicrobial activity of peptides (2-10 kDa) secreted by Saccharomyces cerevisiae Ethanol-Red was evaluated against dermal pathogens using broth microdilution and challenge tests. ACE was assessed using a collagenase activity colorimetric assay, antioxidant activity via spectrophotometric monitoring of nitrotetrazolium blue chloride (NBT) reduction, and anti-inflammatory effects by quantifying TNF-α mRNA in lipopolysaccharides (LPS)-exposed dermal fibroblasts. Wound healing assays involved human fibroblasts, endothelial cells, and dermal keratinocytes. The peptides (2-10 kDa) exhibited antimicrobial activity against 10 dermal pathogens, with the Minimum Inhibitory Concentrations (MICs) ranging from 125 µg/mL for Staphylococcus aureus to 1000 µg/mL for Candida albicans and Streptococcus pyogenes. In the challenge test, peptides at their MICs reduced microbial counts significantly, fulfilling ISO 11930:2019 standards, except against Aspergillus brasiliensis. The peptides combined with MicrocareⓇ SB showed synergy, particularly against C. albicans and A. brasilensis. In vitro, the peptides inhibited collagenase activity by 41.8% and 94.5% at 250 and 1000 µg/mL, respectively, and demonstrated antioxidant capacity. Pre-incubation with peptides decreased TNF-α expression in fibroblasts, indicating anti-inflammatory effects. The peptides do not show to promote or inhibit the angiogenesis of endothelial cells, but are able to attenuate fibrosis, scar formation, and chronic inflammation during the final phases of the wound healing process. The peptides showed antimicrobial, antioxidant, ACE, and anti-inflammatory properties, highlighting their potential as multifunctional bioactive ingredients in skincare, warranting further optimization and exploration in cosmetic applications.

Physical cell-cell contact elicits specific transcriptomic responses in wine yeast species

Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions. These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.

Insights into Molecular Interactions between a GAPDH-Related Fish Antimicrobial Peptide, Analogs Thereof, and Bacterial Membranes

Interactions between SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four analogs thereof with model bacterial membranes were studied using Fourier-transform infrared spectroscopy (FTIR) and molecular dynamics (MD) simulations. MD trajectory analyses showed that the N-terminal segment of the peptide analogs has many contacts with the polar heads of membrane phospholipids, while the central α helix interacts strongly with the hydrophobic core of the membranes. The peptides also had a marked influence on the wave numbers associated with the phase transition of phospholipids organized as liposomes in both the interface and aliphatic chain regions of the infrared spectra, supporting the interactions observed in the MD trajectories. In addition, interesting links were found between peptide interactions with the aliphatic chains of membrane phospholipids, as determined by FTIR and from the MD trajectories, and the membrane permeabilization capacity of these peptide analogs, as previously demonstrated. To summarize, the combined experimental and computational efforts have provided insights into crucial aspects of the interactions between the investigated peptides and bacterial membranes. This work thus makes an original contribution to our understanding of the molecular interactions underlying the antimicrobial activity of these GAPDH-related antimicrobial peptides from Scombridae.

A comparative study to investigate the individual contribution of metabolic and physical interaction on volatiles formation in the mixed fermentation of Torulaspora delbrueckii and Saccharomyces cerevisiae

It is well-known that the co-inoculation of Saccharomyces cerevisiae and non-Saccharomyces strains can modulate and improve the aromatic quality of wine through their multi-level interactions. However, the individual contribution of metabolic interaction (MI) and physical interaction (PI) on wine volatiles remains poorly understood. In this work, we utilized a double-compartment bioreactor to examine the aromatic effect of MI and PI by comparing the volatiles production in Torulaspora delbrueckii and Saccharomyces cerevisiae single fermentations to their mixed fermentations with or without physical separation. Results showed that the PI between T. delbrueckii and S. cerevisiae increased the production of most aroma compounds, especially for acetate esters and volatile fatty acids. In comparison, the MI only promoted a few volatile compounds, including ethyl decanoate, isoamyl acetate, and isobutanol. Noticeably, the MI significantly decreased the levels of ethyl dodecanoate, 2-phenylethyl alcohol, and decanoic acid, which exhibited opposite profiles in PI. Our results indicated that the PI was mainly responsible for the improved volatiles in T. delbrueckii/S. cerevisiae mixed fermentation, while the MI can be targeted to modulate the specific aroma compounds. A thorough understanding of the PI and MI aromatic effect will empower winemakers to accurately and directionally control the volatile profile of the wine, promoting the application of multi-starters to produce diverse styles of wines.

Enhancement of ester biosynthesis in blueberry wines through co-fermentation via cell-cell contact between Torulaspora delbrueckii and Saccharomyces cerevisiae

This study investigated the effects of co-fermentation of T. delbrueckii and S. cerevisiae on the volatile composition and sensory characteristics of blueberry wines. Mixed fermentation led to higher levels of terpenes, higher alcohols, and esters compared to wines fermented with each yeast individually. Conversely, when T. delbrueckii were physically separated from S. cerevisiae in the double-compartment fermenter, contrasting outcomes emerged. The stronger fruity aroma induced by mixed fermentation were linked to higher ester concentrations, including isoamyl acetate, ethyl isovalerate, ethyl hexanoate, and diethyl succinate. The enhanced esters in mixed fermentation can be attributed to the upregulated alcohol acyltransferase activity and the expressions of ACC1, FAS2, ELO1 and ATF1 genes in late fermentation stage via the cell-cell contact between T. delbrueckii and S. cerevisiae. These findings can deepen the understanding of the interaction between non-Saccharomyces and S. cerevisiae in ester production, assisting wineries in effectively controlling wine aroma through mixed fermentations.

Discovering the effect of co-fermentation involving Saccharomyces cerevisiae and Schizosaccharomyces pombe on the sensory quality improvement of mandarin wine based on metabolites and transcriptomic profiles

BACKGROUND

Mandarin wine has high added value, which can extend the industry chain of mandarins with excellent economic results. However, innovative fermentation methods are urgently needed to improve the typical taste and flavor characteristics of mandarin wine. In this study, the effect and underlying mechanism of co-fermentation with Saccharomyces cerevisiae and Schizosaccharomyces pombe on the characteristics of mandarin wine were investigated based on integrated metabolomic and transcriptomic analyses.

RESULTS

In comparison with fermentation with only S. cerevisiae, the mandarin wine produced from co-fermentation with S. cerevisiae and Sc. pombe had a higher pH value, lower malic acid content, and more abundant free amino acids, resulting in better sensory evaluation scores. The introduction of Sc. pombe extended the stage of alcoholic fermentation and enhanced the richness and diversity of volatile compounds, especially floral and fruity aroma compounds, including ethyl hexanoate, ethyl caprylate, ethyl enanthate, 1-heptanol, and phenylethyl alcohol. he significantly differential metabolites and varying genes were mainly found in pathways of glycolysis, pyruvate metabolism, the citrate cycle, and amino acid metabolism.

CONCLUSION

Co-fermentation with S. cerevisiae and Sc. pombe showed advantages in producing distinctive taste and flavor of mandarin wine in comparison with fermentation with only S. cerevisiae. This study can inspire new co-fermentation strategies to improve the sensory quality of mandarin wine. © 2023 Society of Chemical Industry.

RNA viruses, M satellites, chromosomal killer genes, and killer/nonkiller phenotypes in the 100-genomes S. cerevisiae strains

We characterized previously identified RNA viruses (L-A, L-BC, 20S, and 23S), L-A-dependent M satellites (M1, M2, M28, and Mlus), and M satellite-dependent killer phenotypes in the Saccharomyces cerevisiae 100-genomes genetic resource population. L-BC was present in all strains, albeit in 2 distinct levels, L-BChi and L-BClo; the L-BC level is associated with the L-BC genotype. L-BChi, L-A, 20S, 23S, M1, M2, and Mlus (M28 was absent) were in fewer strains than the similarly inherited 2µ plasmid. Novel L-A-dependent phenotypes were identified. Ten M+ strains exhibited M satellite-dependent killing (K+) of at least 1 of the naturally M0 and cured M0 derivatives of the 100-genomes strains; in these M0 strains, sensitivities to K1+, K2+, and K28+ strains varied. Finally, to complement our M satellite-encoded killer toxin analysis, we assembled the chromosomal KHS1 and KHR1 killer genes and used naturally M0 and cured M0 derivatives of the 100-genomes strains to assess and characterize the chromosomal killer phenotypes.

Assessing the Activity under Different Physico-Chemical Conditions, Digestibility, and Innocuity of a GAPDH-Related Fish Antimicrobial Peptide and Analogs Thereof

The antimicrobial activity of SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four chemical analogs thereof was determined under different physicochemical conditions, including different pH values, the presence of monovalent and divalent cations, and after a heating treatment. The toxicity of these five peptides was also studied with hemolytic activity assays, while their stability under human gastrointestinal conditions was evaluated using a dynamic in vitro digestion model and chromatographic and mass spectrometric analyses. The antibacterial activity of all analogs was found to be inhibited by the presence of divalent cations, while monovalent cations had a much less pronounced impact, even promoting the activity of the native SJGAP. The peptides were also more active at acidic pH values, but they did not all show the same stability following a heat treatment. SJGAP and its analogs did not show significant hemolytic activity (except for one of the analogs at a concentration equivalent to 64 times that of its minimum inhibitory concentration), and the two analogs whose digestibility was studied degraded very rapidly once they entered the stomach compartment of the digestion model. This study highlights for the first time the characteristics of antimicrobial peptides from Scombridae or homologous to GAPDH that are directly related to their potential clinical or food applications.

Saccharomyces cerevisiae responds similarly to co-culture or to a fraction enriched in Metschnikowia pulcherrima extracellular vesicles

The recent introduction of non-conventional yeast species as companion wine starters has prompted a growing interest in microbial interactions during wine fermentation. There is evidence of interactions through interference and exploitation competition, as well as interactions depending on physical contact. Furthermore, the results of some transcriptomic analyses suggest interspecific communication, but the molecules or biological structures involved in recognition are not well understood. In this work, we explored extracellular vesicles (EVs) as possible mediators of interspecific communication between wine yeasts. The transcriptomic response of Saccharomyces cerevisiae after 3 h of contact with a fraction enriched in EVs of Metschnikowia pulcherrima was compared with that induced by active M. pulcherrima cells. Interestingly, there is a high level of overlap between the transcriptomic profiles of yeast cells challenged by either M. pulcherrima whole cells or the EV-enriched fraction. The results indicate an upregulation of yeast metabolism in response to competing species (in line with previous results). This finding points to the presence of a signal, in the EV-enriched fraction, that can be perceived by the yeast cells as a cue for the presence of competitors, even in the absence of metabolically active cells of the other species.

Importance of micronutrients and organic nitrogen in fermentations with Torulaspora delbrueckii and Saccharomyces cerevisiae

The current use of non-Saccharomyces yeasts in mixed fermentations increases the relevance of the interactions between yeast species. In this work, the interactions between Saccharomyces cerevisiae and Torulaspora delbrueckii were analyzed. For this purpose, fermentations with and without contact between strains of those yeast species were performed in synthetic must. Fermentation kinetics, yeast growth and dynamics were measured over time. Additionally, the effects of nitrogen and other nutrient supplementations on the mixed fermentations were determined. Our results showed that S. cerevisiae did not always dominate the sequential fermentations, and experiments without yeast contact (in which T. delbrueckii cells were removed from the medium before inoculating S. cerevisiae at 48 h) resulted in stuck fermentations except when the inoculum size was increased (from 2 × 10⁶ to 10⁸ cells/mL) or there was a supplementation of thiamine, zinc and amino acids at the same concentration as initially found in the synthetic must. Our findings highlight the importance of inoculum size and ensuring the availability of enough micronutrients for all yeast species, especially in sequential fermentations.

Impact of Non-Saccharomyces Wine Yeast Strains on Improving Healthy Characteristics and the Sensory Profile of Beer in Sequential Fermentation

The use of non-Saccharomyces yeasts in brewing is a useful tool for developing new products to meet the growing consumer demand for innovative products. Non-Saccharomyces yeasts can be used both in single and in mixed fermentations with Saccharomyces cerevisiae, as they are able to improve the sensory profile of beers, and they can be used to obtain functional beers (with a low ethanol content and melatonin production). The aim of this study was to evaluate this capacity in eight non-Saccharomyces strains isolated from Madrid agriculture. For this purpose, single fermentations were carried out with non-Saccharomyces strains and sequential fermentations with non-Saccharomyces and the commercial strain SafAle S-04. The Wickerhamomyces anomalus strain CLI 1028 was selected in pure culture for brewing beer with a low ethanol content (1.25% (v/v)) for its fruity and phenolic flavours and the absence of wort flavours. The best-evaluated strains in sequential fermentation were CLI 3 (Hanseniaspora vineae) and CLI 457 (Metschnikowia pulcherrima), due to their fruity notes as well as their superior bitterness, body, and balance. Volatile compounds and melatonin production were analysed by GC and HPLC, respectively. The beers were sensory-analysed by a trained panel. The results of the study show the potential of non-Saccharomyces strains in the production of low-alcohol beers, and as a flavour enhancement in sequential fermentation.

Determination of the Relationships between the Chemical Structure and Antimicrobial Activity of a GAPDH-Related Fish Antimicrobial Peptide and Analogs Thereof

The structure–activity relationships and mode of action of synthesized glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-related antimicrobial peptides were investigated. Including the native skipjack tuna GAPDH-related peptide (SJGAP) of 32 amino acid residues (model for the study), 8 different peptide analogs were designed and synthesized to study the impact of net charge, hydrophobicity, amphipathicity, and secondary structure on both antibacterial and antifungal activities. A net positive charge increase, by the substitution of anionic residues or C-terminal amidation, improved the antimicrobial activity of the SJGAP analogs (minimal inhibitory concentrations of 16–64 μg/mL), whereas the alpha helix content, as determined by circular dichroism, did not have a very definite impact. The hydrophobicity of the peptides was also found to be important, especially for the improvement of antifungal activity. Membrane permeabilization assays showed that the active peptides induced significant cytoplasmic membrane permeabilization in the bacteria and yeast tested, but that this permeabilization did not cause leakage of 260 nm-absorbing intracellular material. This points to a mixed mode of action involving both membrane pore formation and targeting of intracellular components. This study is the first to highlight the links between the physicochemical properties, secondary structure, antimicrobial activity, and mechanism of action of antimicrobial peptides from scombrids or homologous to GAPDH.

Identification of Antibacterial Peptide Candidates Encrypted in Stress-Related and Metabolic Saccharomyces cerevisiae Proteins

The protein-rich nature of Saccharomyces cerevisiae has led this yeast to the spotlight concerning the search for antimicrobial peptides. Herein, a <10 kDa peptide-rich extract displaying antibacterial activity was obtained through the autolysis of yeast biomass under mild thermal treatment with self-proteolysis by endogenous peptidases. Estimated IC₅₀ for the peptide pools obtained by FPLC gel filtration indicated improved antibacterial activities against foodborne bacteria and bacteria of clinical interest. Similarly, the estimated cytotoxicity concentrations against healthy human fibroblasts, alongside selective indices ≥10, indicates the fractions are safe, at least in a mixture format, for human tissues. Nano-LC-MS/MS analysis revealed that the peptides in FPLC fractions could be derived from both induced-proteolysis and proteasome activity in abundant proteins, up-regulated under stress conditions during S. cerevisiae biomass manufacturing, including those coded by TDH1/2/3, HSP12, SSA1/2, ADH1/2, CDC19, PGK1, PPI1, PDC1, and GMP1, as well as by other non-abundant proteins. Fifty-eight AMP candidate sequences were predicted following an in silico analysis using four independent algorithms, indicating their possible contribution to the bacterial inactivation observed in the peptides pool, which deserve special attention for further validation of individual functionality. S. cerevisiae-biomass peptides, an unconventional but abundant source of pharmaceuticals, may be promissory adjuvants to treat infectious diseases that are poorly sensitive to conventional antibiotics.

Phenotypic characterization of cell-to-cell interactions between two yeast species during alcoholic fermentation

Microbial multispecies ecosystems are responsible for many biotechnological processes and are particularly important in food production. In wine fermentations, in addition to the natural microbiota, several commercially relevant yeast species may be co-inoculated to achieve specific outcomes. However, such multispecies fermentations remain largely unpredictable because of multilevel interactions between naturally present and/or co-inoculated species. Understanding the nature of such interactions has therefore become essential for successful implementation of such strategies. Here we investigate interactions between strains of Saccharomyces cerevisiae and Lachancea thermotolerans. Co-fermentations with both species sharing the same bioreactor (physical contact) were compared to co-fermentations with physical separation between the species in a membrane bioreactor ensuring free exchange of metabolites. Yeast culturability, viability and the production of core metabolites were monitored. The previously reported negative interaction between these two yeast species was confirmed. Physical contact greatly reduced the culturability and viability of L. thermotolerans and led to earlier cell death, compared to when these yeasts were co-fermenting without cell-cell contact. In turn, in the absence of cell-cell contact, L. thermotolerans metabolic activity led to an earlier decline in culturability in S. cerevisiae. Cell-cell contact did not result in significant differences in the major fermentation metabolites ethanol, acetic acid and lactic acid, but impacted on the production of some volatile compounds.

Saccharomyces cerevisiae biomass as a source of next-generation food preservatives: Evaluating potential proteins as a source of antimicrobial peptides

Saccharomyces cerevisiae is the main biotechnological tool for the production of Baker's or Brewer's biomasses, largely applied in beverage and fermented-food production. Through its gene expression reprogramming and production of compounds that inactivate the growth of other microorganisms, S. cerevisiae is able to grow in adverse environments and in complex microbial consortia, as in fruit pulps and root flour fermentations. The distinct set of up-regulated genes throughout yeast biomass propagation includes those involved in sugar fermentation, ethanol metabolization, and in protective responses against abiotic stresses. These high abundant proteins are precursors of several peptides with promising health-beneficial activities such as antihypertensive, antioxidant, antimicrobial, immunomodulatory, anti-obesity, antidiabetes, and mitogenic properties. An in silico investigation of these S. cerevisiae derived peptides produced during yeast biomass propagation or induced by physicochemical treatments were performed using four algorithms to predict antimicrobial candidates encrypted in abundantly expressed stress-related proteins encoded by different genes like AHP1, TSA1, HSP26, SOD1, HSP10, and UTR2, or metabolic enzymes involved in carbon source utilization, like ENO1/2, TDH1/2/3, ADH1/2, FBA1, and PDC1. Glyceraldehyde-3-phosphate dehydrogenase and enolase II are noteworthy precursor proteins, since they exhibited the highest scores concerning the release of antimicrobial peptide candidates. Considering the set of genes upregulated during biomass propagation, we conclude that S. cerevisiae biomass, a food-grade product consumed and marketed worldwide, should be considered a safe and nonseasonal source for designing next-generation bioactive agents, especially protein encrypting antimicrobial peptides that display broad spectra activity and could reduce the emergence of microbial resistance while also avoiding cytotoxicity.

Mechanisms Involved in Interspecific Communication between Wine Yeasts

In parallel with the development of non-Saccharomyces starter cultures in oenology, a growing interest has developed around the interactions between the microorganisms involved in the transformation of grape must into wine. Nowadays, it is widely accepted that the outcome of a fermentation process involving two or more inoculated yeast species will be different from the weighted average of the corresponding individual cultures. Interspecific interactions between wine yeasts take place on several levels, including interference competition, exploitation competition, exchange of metabolic intermediates, and others. Some interactions could be a simple consequence of each yeast running its own metabolic programme in a context where metabolic intermediates and end products from other yeasts are present. However, there are clear indications, in some cases, of specific recognition between interacting yeasts. In this article we discuss the mechanisms that may be involved in the communication between wine yeasts during alcoholic fermentation.

GAPDH siRNA Regulates SH-SY5Y Cell Apoptosis Induced by Exogenous α-Synuclein Protein

The transport mechanism of intestinal α-synuclein to the central nervous system has become a new hot topic in Parkinson's disease (PD) research. It is worth noting that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been reported to be involved in the pathogenesis of PD. After silencing GAPDH expression by GAPDH siRNA, the normal human intestinal epithelial crypt-like (HIEC) and human SH-SY5Y neuroblastoma cell lines were co-cultured with Escherichia coli cells which were transfected with an α-synuclein overexpression plasmid. The levels of autophagy-related proteins (BECN1, ATG5, LC3A/B and p62) were determined by Western blot analysis. Changes in pro-apoptosis protein levels and flow cytometry analysis were used to assess cell apoptosis and relative intracellular ATP concentration was measured. Oxidative stress was assessed by measuring the levels of reactive oxygen species (ROS) using 2',7'-dichlorofluorescein diacetate (DCFH-DA), thiobarbituric acid-reactive substances (TBARS), and antioxidant capacity was assessed by measuring the glutathione (GSH) levels and superoxide dismutase (SOD) activity. The silencing of the expression of GAPDH pre-knockdown was found to reduce the intracellular levels of ROS and lipid peroxidation, enhance autophagy activity, thereby reducing the cell injury, apoptosis and necrosis induced by exogenous α-synuclein protein in SH-SY5Y cells. This study identifies a new therapeutic target of exogenous α-synuclein protein induced SH-SY5Y cell injury and improves our understanding of the pathophysiological role of GAPDH in vitro.

The ecology of wine fermentation: a model for the study of complex microbial ecosystems

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.

Enzymatic Analysis of Yeast Cell Wall-Resident GAPDH and Its Secretion

In yeast, many proteins are found in both the cytoplasmic and extracellular compartments, and consequently it can be difficult to distinguish nonconventional secretion from cellular leakage. Therefore, we monitored the extracellular glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity of intact cells as a specific marker for nonconventional secretion. Extracellular GAPDH activity was proportional to the number of cells assayed, increased with incubation time, and was dependent on added substrates. Preincubation of intact cells with 100 μM dithiothreitol increased the reaction rate, consistent with increased access of the enzyme after reduction of cell wall disulfide cross-links. Such treatment did not increase cell permeability to propidium iodide, in contrast to effects of higher concentrations of reducing agents. An amine-specific membrane-impermeant biotinylation reagent specifically inactivated extracellular GAPDH. The enzyme was secreted again after a 30- to 60-min lag following the inactivation, and there was no concomitant increase in propidium iodide staining. There were about 4 × 10⁴ active GAPDH molecules per cell at steady state, and secretion studies showed replenishment to that level 1 h after inactivation. These results establish conditions for specific quantitative assays of cell wall proteins in the absence of cytoplasmic leakage and for subsequent quantification of secretion rates in intact cells.IMPORTANCE Eukaryotic cells secrete many proteins, including many proteins that do not follow the classical secretion pathway. Among these, the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is unexpectedly found in the walls of yeasts and other fungi and in extracellular space in mammalian cell cultures. It is difficult to quantify extracellular GAPDH, because leakage of just a little of the very large amount of cytoplasmic enzyme can invalidate the determinations. We used enzymatic assays of intact cells while also maintaining membrane integrity. The results lead to estimates of the amount of extracellular enzyme and its rate of secretion to the wall in intact cells. Therefore, enzyme assays under controlled conditions can be used to investigate nonconventional secretion more generally.

Use of Hanseniaspora guilliermondii and Hanseniaspora opuntiae to enhance the aromatic profile of beer in mixed-culture fermentation with Saccharomyces cerevisiae

Beer production is predominantly carried out by Saccharomyces species, such as S. cerevisiae and S. pastorianus. However, the introduction of non-Saccharomyces yeasts in the brewing process is now seen as a promising strategy to improve and differentiate the organoleptic profile of beer. In this study, 17 non-Saccharomyces strains of 12 distinct species were isolated and submitted to a preliminary sensory evaluation to determine their potential for beer bioflavouring. Hanseniaspora guilliermondii IST315 and H. opuntiae IST408 aroma profiles presented the highest acceptability and were described as having 'fruity' and 'toffee' notes, respectively. Their presence in mixed-culture fermentations with S. cerevisiae US-05 did not influence attenuation and ethanol concentration of beer but had a significant impact in its volatile composition. Notably, while both strains reduced the total amount of ethyl esters, H. guilliermondii IST315 greatly increased the concentration of acetate esters, especially when sequentially inoculated, leading to an 8.2-fold increase in phenylethyl acetate ('rose', 'honey' aroma) in the final beverage. These findings highlight the importance of non-Saccharomyces yeasts in shaping the aroma profile of beer and suggest a role for Hanseniaspora spp. in improving it.

Phenotypic and transcriptional analysis of Saccharomyces cerevisiae during wine fermentation in response to nitrogen nutrition and co-inoculation with Torulaspora delbrueckii

Nitrogen content of grape musts strongly impacts on fermentation performance and wine metabolite production. As nitrogen is a limiting nutrient in most grape musts, nitrogen supplementation is a common practice that ensures yeast growth during fermentation. However, preferred nitrogen sources -as ammonium- repress the genes related to alternative nitrogen sources consumption, usually involved in aromatic compounds production. Here, we describe the effect of high ammonium doses in Saccharomyces cerevisiae fermentation performance and wine properties, and how it is affected by yeast co-inoculation in mixed (S. cerevisiae + Torulaspora delbrueckii) fermentations. In addition, an RNA-seq analysis allowed us to study the S. cerevisiae transcriptional response to ammonium nutrition and yeast interaction, demonstrating that T. delbrueckii presence affects the global S. cerevisiae transcriptional response, reducing ammonium effects at both phenotypic -fermentation kinetics and metabolite production- and transcriptional levels, under experimental conditions.

Can community-based signalling behaviour in Saccharomyces cerevisiae be called quorum sensing? A critical review of the literature

Quorum sensing is a well-described mechanism of intercellular signalling among bacteria, which involves cell-density-dependent chemical signal molecules. The concentration of these quorum-sensing molecules increases in proportion to cell density until a threshold value is exceeded, which triggers a community-wide response. In this review, we propose that intercellular signalling mechanisms can be associated with a corresponding ecological interaction type based on similarities between how the interaction affects the signal receiver and producer. Thus, we do not confine quorum sensing, a specific form of intercellular signalling, to only cooperative behaviours. Instead, we define it as cell-density-dependent responses that occur at a critical concentration of signal molecules and through a specific signalling pathway. For fungal species, the medically important yeast Candida albicans has a well-described quorum sensing system, while this system is not well described in Saccharomyces cerevisiae, which is involved in food and beverage fermentations. The more precise definition for quorum sensing proposed in this review is based on the studies suggesting that S. cerevisiae may undergo intercellular signalling through quorum sensing. Through this lens, we conclude that there is a lack of evidence to support a specific signalling mechanism and a critical signal concentration of these behaviours in S. cerevisiae, and, thus, these features require further investigation.

Peer pressure: evolutionary responses to biotic pressures in wine yeasts

In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.

Yeast-Yeast Interactions: Mechanisms, Methodologies and Impact on Composition

During the winemaking process, alcoholic fermentation is carried out by a consortium of yeasts in which interactions occurs. The consequences of these interactions on the wine matrix have been widely described for several years with the aim of controlling the winemaking process as well as possible. In this review, we highlight the wide diversity of methodologies used to study these interactions, and their underlying mechanisms and consequences on the final wine composition and characteristics. The wide variety of matrix parameters, yeast couples, and culture conditions have led to contradictions between the results of the different studies considered. More recent aspects of modifications in the composition of the matrix are addressed through different approaches that have not been synthesized recently. Non-volatile and volatile metabolomics, as well as sensory analysis approaches are developed in this paper. The description of the matrix composition modification does not appear sufficient to explain interaction mechanisms, making it vital to take an integrated approach to draw definite conclusions on them.

Proteomics insights into the responses of Saccharomyces cerevisiae during mixed-culture alcoholic fermentation with Lachancea thermotolerans

The response of Saccharomyces cerevisiae to cocultivation with Lachancea thermotolerans during alcoholic fermentations has been investigated using tandem mass tag (TMT)-based proteomics. At two key time-points, S. cerevisiae was sorted from single S. cerevisiae fermentations and from mixed fermentations using flow cytometry sorting. Results showed that the purity of sorted S. cerevisiae was above 96% throughout the whole mixed-culture fermentation, thereby validating our sorting methodology. By comparing protein expression of S. cerevisiae with and without L. thermotolerans, 26 proteins were identified as significantly regulated proteins at the early death phase (T1), and 32 significantly regulated proteins were identified at the late death phase (T2) of L. thermotolerans in mixed cultures. At T1, proteins involved in endocytosis, increasing nutrient availability, cell rescue and resistance to stresses were upregulated, and proteins involved in proline synthesis and apoptosis were downregulated. At T2, proteins involved in protein synthesis and stress responses were up- and downregulated, respectively. These data indicate that S. cerevisiae was stressed by the presence of L. thermotolerans at T1, using both defensive and fighting strategies to keep itself in a dominant position, and that it at T2 was relieved from stress, perhaps increasing its enzymatic machinery to ensure better survival.

Genome sequence of the non-conventional wine yeast Hanseniaspora guilliermondii UTAD222 unveils relevant traits of this species and of the Hanseniaspora genus in the context of wine fermentation

Hanseanispora species, including H. guilliermondii, are long known to be abundant in wine grape-musts and to play a critical role in vinification by modulating, among other aspects, the wine sensory profile. Despite this, the genetics and physiology of Hanseniaspora species remains poorly understood. The first genomic sequence of a H. guilliermondii strain (UTAD222) and the discussion of its potential significance are presented in this work. Metabolic reconstruction revealed that H. guilliermondii is not equipped with a functional gluconeogenesis or glyoxylate cycle, nor does it harbours key enzymes for glycerol or galactose catabolism or for biosynthesis of biotin and thiamine. Also, no fructose-specific transporter could also be predicted from the analysis of H. guilliermondii genome leaving open the mechanisms underlying the fructophilic character of this yeast. Comparative analysis involving H. guilliermondii, H. uvarum, H. opuntiae and S. cerevisiae revealed 14 H. guilliermondii-specific genes (including five viral proteins and one β-glucosidase). Furthermore, 870 proteins were only found within the Hanseniaspora proteomes including several β-glucosidases and decarboxylases required for catabolism of biogenic amines. The release of H. guilliermondii genomic sequence and the comparative genomics/proteomics analyses performed, is expected to accelerate research focused on Hanseniaspora species and to broaden their application in the wine industry and in other bio-industries in which they could be explored as cell factories.

Biocontrol of Brettanomyces/Dekkera bruxellensis in alcoholic fermentations using saccharomycin-overproducing Saccharomyces cerevisiae strains

Microbial contamination of alcoholic fermentation processes (e.g. winemaking and fuel-ethanol production) is a serious problem for the industry since it may render the product unacceptable and/or reduce its productivity, leading to large economic losses. Brettanomyces/Dekkera bruxellensis is one of the most dangerous microbial contaminant of ethanol industrial fermentations. In the case of wine, this yeast species can produce phenolic compounds that confer off-flavours to the final product. In fuel-ethanol fermentations, D. bruxellensis is a persistent contaminant that affects ethanol yields and productivities. We recently found that Saccharomyces cerevisiae secretes a biocide, which we named saccharomycin, composed of antimicrobial peptides (AMPs) derived from the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Saccharomycin is active against several wine-related yeast species, namely D. bruxellensis. However, the levels of saccharomycin naturally secreted by S. cerevisiae during alcoholic fermentation are not sufficient to ensure the complete death of D. bruxellensis. Therefore, the aim of the present work was to construct genetically modified S. cerevisiae strains to overproduce these GAPDH-derived AMPs. The expression levels of the nucleotides sequences encoding the AMPs were evaluated in the modified S. cerevisiae strains by RT-qPCR, confirming the success of the recombinant approach. Furthermore, we confirmed by immunological tests that the modified S. cerevisiae strains secreted higher amounts of the AMPs by comparison with the non-modified strain, inducing total death of D. bruxellensis during alcoholic fermentations.

Cell-to-cell contact mechanism modulates Starmerella bacillaris death in mixed culture fermentations with Saccharomyces cerevisiae

The use of mixed culture fermentations with selected Starmerella bacillaris and Saccharomyces cerevisiae strains is gaining winemaking attention, mainly due to their ability to enhance particular characteristics in the resulting wines. In this context, yeast interspecies interactions during fermentation have a fundamental role to determine the desired product characteristics, since they may modulate yeast growth and as a consequence metabolite production. In order to get an insight into these interactions, the growth and death kinetics of the abovementioned species were investigated in pure and mixed culture fermentations, using cv. Nebbiolo grape must. Trials were conducted in flasks but also in a double-compartment fermentation system in which cells of the two species were kept separate by a filter membrane. Although the two species had similar growth pattern during the first days of fermentation, Starm. bacillaris died earlier when tested in the flask than in the double-compartment fermentor. The early death of Starm. bacillaris seemed to be not caused by nutrient limitation nor by accumulation of growth inhibitory compounds (which were not measured in the present study). Rather, cell-to-cell contact mechanism, dependent on the presence of viable S. cerevisiae cells, appears to be responsible for the observations made. These results contribute to better understand the factors that influence Starm. bacillaris death during wine fermentations.