Analysis of the NCR Mechanisms in Hanseniaspora vineae and Saccharomyces cerevisiae During Winemaking

Assessment of breeding nuclei contributions to the genetic diversity and population structure of the Cyprus Chios sheep

Cyprus, facing climate change and desertification, has Europe's second highest population growth. Halloumi cheese's Protected Designation of Origin status boosted goat and sheep milk demand. Optimizing primary sector production is key to balancing food production and environmental sustainability. The present study aims to explore the genetic diversity and population structure of Cyprus Chios sheep, as well as the impact of existing breeding nuclei on the breed's gene pool. Two breeding nuclei aiming to preserve genetic diversity and boost local milk production and four private farms were sampled. Genome-wide data using Illumina 50 K arrays were generated, analyzing over 1000 animals from six farms. At least three distinct genetic groups were identified, two of which are represented by the nuclei's distinct genetic profiles and a third was found in private farms. Calculated metrics indicate a negative correlation of gene flow with geographic distance in case of the Eastern nucleus. Presented results support recent, though limited inbreeding (mean FROH=0.046), compared to other commercial breeds. Estimated effective population size reveals a stabilizing trend to a relatively high number (Ne ~ 200) which indicates relatively high diversity that allows further genetic improvement. Revealed genomic diversity highlights the necessity of such exploration before effectively implementing genomic evaluation programs.

Research progress on the function and regulatory pathways of amino acid permeases in fungi

Nitrogen sources are pivotal for the formation of fungal mycelia and the biosynthesis of metabolites, playing a crucial role in the growth and development of fungi. Amino acids are integral to protein construction, constitute an essential nitrogen source for fungi. Fungi actively uptake amino acids from their surroundings, a process that necessitates the involvement of amino acid permeases (AAPs) located on the plasma membrane. By sensing the intracellular demand for amino acids and their extracellular availability, fungi activate or suppress relevant pathways to precisely regulate the genes encoding these transporters. This review aims to illustrate the function of fungal AAPs on uptake of amino acids and the effect of AAPs on fungal growth, development and virulence. Additionally, the complex mechanisms to regulate expression of aaps are elucidated in mainly Saccharomyces cerevisiae, including the Ssy1-Ptr3-Ssy5 (SPS) pathway, the Nitrogen Catabolite Repression (NCR) pathway, and the General Amino Acid Control (GAAC) pathway. However, the physiological roles of AAPs and their regulatory mechanisms in other species, particularly pathogenic fungi, merit further exploration. Gaining insights into these aspects could reveal how AAPs facilitate fungal adaptation and survival under diverse stress conditions, shedding light on their potential impact on fungal biology and pathogenicity.

Exploring future applications of the apiculate yeast Hanseniaspora

As a metaphor, lemons get a bad rap; however the proverb 'if life gives you lemons, make lemonade' is often used in a motivational context. The same could be said of Hanseniaspora in winemaking. Despite its predominance in vineyards and grape must, this lemon-shaped yeast is underappreciated in terms of its contribution to the overall sensory profile of fine wine. Species belonging to this apiculate yeast are known for being common isolates not just on grape berries, but on many other fruits. They play a critical role in the early stages of a fermentation and can influence the quality of the final product. Their deliberate addition within mixed-culture fermentations shows promise in adding to the complexity of a wine and thus provide sensorial benefits. Hanseniaspora species are also key participants in the fermentations of a variety of other foodstuffs ranging from chocolate to apple cider. Outside of their role in fermentation, Hanseniaspora species have attractive biotechnological possibilities as revealed through studies on biocontrol potential, use as a whole-cell biocatalyst and important interactions with Drosophila flies. The growing amount of 'omics data on Hanseniaspora is revealing interesting features of the genus that sets it apart from the other Ascomycetes. This review collates the fields of research conducted on this apiculate yeast genus.

Chromatin regulator Ahc1p co-regulates nitrogen metabolism via interactions with multiple transcription factors in Saccharomyces cerevisiae

Chromatin regulation is an important gene expression/regulation system, but little is known about how it affects nitrogen metabolism in Saccharomyces cerevisiae. A previous study demonstrated the regulatory role of the chromatin regulator Ahc1p on multiple key genes of nitrogen metabolism in S. cerevisiae, but the regulatory mechanism remains unknown. In this study, multiple key nitrogen metabolism genes directly regulated by Ahc1p were identified, and the transcription factors interacting with Ahc1p were analyzed. It was ultimately found that Ahc1p may regulate some key nitrogen metabolism genes in two ways. First, Ahc1p acts as a co-factor and is recruited with transcription factors such as Rtg3p or Gcr1p to facilitate transcription complex binding to target gene core promoters and promote transcription initiation. Second, Ahc1p binds at enhancers to promote the transcription of target genes in concert with transcription factors. This study furthers the understanding of the regulatory network of nitrogen metabolism in S. cerevisiae from an epigenetic perspective.

Gene co-expression network analysis reveals the positive impact of endocytosis and mitochondria-related genes over nitrogen metabolism in Saccharomyces cerevisiae

Nitrogen metabolism is essential for most cellular activities. Therefore, a deep understanding of its regulatory mechanisms is necessary for the efficient utilization of nitrogen sources for Saccharomyces cerevisiae. In this study, a gene co-expression network was constructed for S. cerevisiae S288C with different nitrogen sources. From this, a key gene co-expression module related to nitrogen source preference utilization was obtained, and 10 hub genes centrally located in the co-expression network were identified. Functional studies verified that the endocytosis-related genes CAP1 and END3 significantly increased the utilization of multiple non-preferred amino acids and reduced the accumulation of the harmful nitrogen metabolite precursor urea by regulating amino acid transporters and TOR pathway. The mitochondria-related gene ATP12, MRPL22, MRP1 and NAM9 significantly increased the utilization of multiple non-preferred amino acids and reduced accumulation of the urea by coordinately regulating nitrogen catabolism repression, Ssy1p-Ptr3p-Ssy5p signaling sensor system, amino acid transporters, TOR pathway and urea metabolism-related pathways. Furthermore, these data revealed the potential positive effects of endocytosis and mitochondrial ribosomes protein translation on nitrogen source preference. This study provides new analytical perspectives for complex regulatory networks involving nitrogen metabolism in S. cerevisiae.

A peculiar cell cycle arrest at g2/m stage during the stationary phase of growth in the wine yeas Hanseniaspora vineae

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Cell cycle progress variations among Hanseniaspora species.

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H. vineae shows an unusual cell cycle progress.

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H. vineae undergoes G2/M arrest in stationary phase.

Yeasts of the genus Hanseniaspora gained notoriety in the last years due to their contribution to wine quality, and their loss of several genes, mainly related to DNA repair and cell cycle processes. Based on genomic data from many members of this genus, they have been classified in two well defined clades: the “faster-evolving linage” (FEL) and the “slower-evolving lineage” (SEL). In this context, we had detected that H. vineae exhibited a rapid loss of cell viability in some conditions during the stationary phase compared to H. uvarum and S. cerevisiae. The present work aimed to evaluate the viability and cell cycle progression of representatives of Hanseniaspora species along their growth in an aerobic and discontinuous system. Cell growth, viability and DNA content were determined by turbidity, Trypan Blue staining, and flow cytometry, respectively. Results showed that H. uvarum and H. opuntiae (representing FEL group), and H. osmophila (SEL group) exhibited a typical G1/G0 (1C DNA) arrest during the stationary phase, as S. cerevisiae. Conversely, the three strains studied here of H. vineae (SEL group) arrested at G2/M stages of cell cycle (2C DNA), and lost viability rapidly when enter the stationary phase. These results showed that H. vineae have a unique cell cycle behavior that will contribute as a new eukaryotic model for future studies of genetic determinants of yeast cell cycle control and progression.

The impact of carbon and nitrogen catabolite repression in microorganisms

Organisms have cellular machinery that is focused on optimum utilization of resources to maximize growth and survival depending on various environmental and developmental factors. Catabolite repression is a strategy utilized by various species of bacteria and fungi to accommodate changes in the environment such as the depletion of resources, or an abundance of less-favored nutrient sources. Catabolite repression allows for the rapid use of certain substrates like glucose over other carbon sources. Effective handling of carbon and nitrogen catabolite repression in microorganisms is crucial to outcompete others in nutrient limiting conditions. Investigations into genes and proteins linked to preferential uptake of different nutrients under various environmental conditions can aid in identifying regulatory mechanisms that are crucial for optimum growth and survival of microorganisms. The exact time and way bacteria and fungi switch their utilization of certain nutrients is of great interest for scientific, industrial, and clinical reasons. Catabolite repression is of great significance for industrial applications that rely on microorganisms for the generation of valuable bio-products. The impact catabolite repression has on virulence of pathogenic bacteria and fungi and disease progression in hosts makes it important area of interest in medical research for the prevention of diseases and developing new treatment strategies. Regulatory networks under catabolite repression exemplify the flexibility and the tremendous diversity that is found in microorganisms and provides an impetus for newer insights into these networks.

Downregulation of the broad-specificity amino acid permease Agp1 mediated by the ubiquitin ligase Rsp5 and the arrestin-like protein Bul1 in yeast

Most of plasma membrane transporters are downregulated by ubiquitination-dependent endocytosis to avoid the excess uptake of their substrates. In Saccharomyces cerevisiae, ubiquitination of transporters is mediated by the HECT-type ubiquitin ligase Rsp5. We report here a mechanism underlying the substrate-induced endocytosis of the broad-specificity amino acid permease Agp1. First, we found that Agp1 underwent ubiquitination and endocytosis in response to the addition of excess asparagine, which is a substrate of Agp1. Moreover, the substrate-induced internalization of Agp1 was dependent on the ubiquitination activity of Rsp5. Since Rsp5 requires α-arrestin family proteins as adaptors to bind with substrates, we next developed a method of genetic screening to identify adaptor proteins for Agp1 endocytosis. This screening and biochemical analysis revealed that Bul1, but not its paralogue Bul2, was essential for the substrate-induced endocytosis of Agp1. Our results support that the substrate-induced endocytosis of Agp1 requires Rsp5 and Bul1.

Exploration of yeast communities in fresh coconut, palmyra, and nipa palm saps and ethanol-fermenting ability of isolated yeasts

This study aimed to explore communities and the ethanol-fermenting ability of yeasts in fresh coconut, palmyra, and nipa palm saps. From the 90 samples of coconut, palmyra, and nipa palm saps, 204 yeast isolates were isolated and identified as 15 species in the phylum Ascomycota and a species (one strain) in Basidiomycota. Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Lachancea thermotolerans were found in the saps of all three palm species. Candida tropicalis and Pichia kudriavzevii were obtained from the coconut and palmyra palm saps, Hanseniaspora vineae, Lachancea fermentati, and Pichia manshurica were present in the coconut and nipa palm saps, whereas Torulaspora delbrueckii was found in the palmyra and nipa palm saps. The species with the highest occurrence in the saps of coconut, palmyra, and nipa palms was S. cerevisiae with 76.67%, 86.70%, and 100% frequency of occurrence, respectively. Using principal coordinates analysis for ordination, no marked difference was observed in the yeast communities from the saps of the three palm species. A total of 199 isolates were found to possess ethanol-fermentation ability when cultivated using shake flask in 160 g/L of glucose medium at 28°C for 48 h. Lachancea fermentati YSP-383, isolated from nipa palm sap, produced the highest amount of ethanol (76.74 g/L). Twenty-six isolates of Candida sanyaensis (1), C. tropicalis (1), H. guilliermondii (7), L. fermentati (8), L. thermotolerans (1), Pichia kudriavzevii (2), and S. cerevisiae (6) produced high amounts of ethanol ranging from 69.57 to 76.74 g/L. The result demonstrated that yeasts in the palm saps could play roles in the natural fermentation of palm saps.

Impact of Hanseniaspora Vineae in Alcoholic Fermentation and Ageing on Lees of High-Quality White Wine

Hanseniaspora vineae is an apiculate yeast that plays a significant role at the beginning of fermentation, and it has been studied for its application in the improvement of the aromatic profile of commercial wines. This work evaluates the use of H. vineae in alcoholic fermentation compared to Saccharomyces cerevisiae and in ageing on the lees process (AOL) compared to Saccharomyces and non-Saccharomyces yeasts. The results indicated that there were not significant differences in basic oenological parameters. H. vineae completed the fermentation until 11.9% v/v of ethanol and with a residual sugars content of less than 2 g/L. Different aroma profiles were obtained in the wines, with esters concentration around 90 mg/L in H. vineae wines. Regarding the AOL assay, the hydroalcoholic solutions aged with H. vineae lees showed significantly higher absorbance values at 260 (nucleic acids) and 280 nm (proteins) compared to the other strains. However, non-significant differences were found in the polysaccharide content at the end of the ageing process were found compared to the other yeast species, with the exception of Schizosaccharomyces pombe that released around 23.5 mg/L of polysaccharides in hydroalcoholic solution. The use of H. vineae by the wineries may be a viable method in fermentation and AOL to improve the quality of white wines.

Effect of Several Nutrients and Environmental Conditions on Intracellular Melatonin Synthesis in Saccharomyces cerevisiae

Melatonin is a bioactive compound that is present in fermented beverages and has been described to be synthesized by yeast during alcoholic fermentation. The aim of this study was to assess the capacity of intracellular and extracellular melatonin production by different Saccharomyces strains from diverse food origin and to study the effects of different fermentation parameters, such as sugar and nitrogen concentration, temperature or initial population, on melatonin production using a synthetic grape must medium. Melatonin from fermentation samples was analyzed by liquid chromatography mass spectrometry. Intracellular melatonin synthesis profile did not present differences between yeast strains. However, extracellular melatonin production depended on the yeast origin. Thus, we suggest that melatonin production and secretion during the different yeast growth phases follows a species-specific pattern. Other parameters that affected the fermentation process such as sugar content and low temperature had an impact on intracellular melatonin production profile, as well as the melatonin content within the cell. This study reports the effect of several conditions on the melatonin synthesis profile, highlighting its possible role as a signal molecule.

Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation

Spontaneous wine fermentation is characterized by yeast population evolution, modulated by complex physical and metabolic interactions amongst various species. The contribution of any given species to the final wine character and aroma will depend on its numerical persistence during the fermentation process. Studies have primarily evaluated the effect of physical and chemical factors such as osmotic pressure, pH, temperature and nutrient availability on mono- or mixed-cultures comprising 2-3 species, but information about how interspecies ecological interactions in the wine fermentation ecosystem contribute to population dynamics remains scant. Therefore, in the current study, the effect of temperature and sulphur dioxide (SO2) on the dynamics of a multi-species yeast consortium was evaluated in three different matrices including synthetic grape juice, Chenin blanc and Grechetto bianco. The population dynamics were affected by temperature and SO2, reflecting differences in stress resistance and habitat preferences of the different species and influencing the production of most volatile aroma compounds. Evidently at 15 °C and in the absence of SO2 non-Saccharomyces species were dominant, whereas at 25 °C and when 30 mg/L SO2 was added S. cerevisiae dominated. Population growth followed similar patterns in the three matrices independently of the conditions. The data show that fermentation stresses lead to an individual response of each species, but that this response is strongly influenced by the interactions between species within the ecosystem. Thus, our data suggest that ecological interactions, and not only physico-chemical conditions, are a dominant factor in determining the contribution of individual species to the outcome of the fermentation.

Nitrogen Preferences during Alcoholic Fermentation of Different Non-Saccharomyces Yeasts of Oenological Interest

Non-Saccharomyces yeasts have long been considered spoilage microorganisms. Currently, oenological interest in those species is increasing, mostly due to their positive contribution to wine quality. In this work, the fermentative capacity and nitrogen consumption of several non-Saccharomyces wine yeast (Torulaspora delbrueckii, Lachancea thermotolerans, Starmerella bacillaris, Hanseniaspora uvarum, and Metschnikowia pulcherrima) were analyzed. For this purpose, synthetic must with three different nitrogen compositions was used: a mixture of amino acids and ammonium, only organic or inorganic nitrogen. The fermentation kinetics, nitrogen consumption, and yeast growth were measured over time. Our results showed that the good fermentative strains, T. delbrueckii and L. thermotolerans, had high similarities with Saccharomyces cerevisiae in terms of growth, fermentation profile, and nitrogen assimilation preferences, although L. thermotolerans presented an impaired behavior when only amino acids or ammonia were used, being strain-specific. M. pulcherrima was the non-Saccharomyces strain least affected by the nitrogen composition of the medium. The other two poor fermentative strains, H. uvarum and S. bacillaris, behaved similarly regarding amino acid uptake, which occurred earlier than that of the good fermentative species in the absence of ammonia. The results obtained in single non-Saccharomyces fermentations highlighted the importance of controlling nitrogen requirements of the wine yeasts, mainly in sequential fermentations, in order to manage a proper nitrogen supplementation, when needed.

Nitrogen sources preferences of non-Saccharomyces yeasts to sustain growth and fermentation under winemaking conditions

Wine-related non-Saccharomyces yeasts are becoming more widely used in oenological practice for their ability to confer wine a more complex satisfying aroma, but their metabolism remains unknown. Our study explored the nitrogen utilisation profile of three popular non-Saccharomyces species, Torulaspora delbrueckii, Metschnikowia pulcherrima and Metschnikowia fructicola. The nitrogen source preferences to support growth and fermentation as well as the uptake order of different nitrogen sources during wine fermentation were investigated. While T. delbrueckii and S. cerevisiae strains shared the same nitrogen source preferences, Metschnikowia sp. Displayed a lower capacity to efficiently use the preferred nitrogen compounds, but were able to assimilate a wider range of amino acids. During alcoholic fermentation, the non-Saccharomyces strains consumed different nitrogen sources in a similar order as S. cerevisiae, but not as quickly. Furthermore, when all the nitrogen sources were supplied in the same amount, their assimilation order was similarly affected for both S. cerevisiae and non-Saccharomyces strains. Under this condition, the rate of nitrogen source consumption of non-Saccharomyces strains and S. cerevisiae was comparable. Overall, this study expands our understanding about the preferences and consumption rates of individual nitrogen sources by the investigated non-Saccharomyces yeasts in a wine environment. This knowledge provides useful information for a more efficient exploitation of non-Saccharomyces strains that improves the management of the wine fermentation.

Influence of nitrogen status in wine alcoholic fermentation

Nitrogen is an essential nutrient for yeast during alcoholic fermentation. Nitrogen is involved in the biosynthesis of protein, amino acids, nucleotides, and other metabolites, including volatile compounds. However, recent studies have called several mechanisms that regulate its role in biosynthesis into question. An initial focus on S. cerevisiae has highlighted that the concept of "preferred" versus "non-preferred" nitrogen sources is extremely variable and strain-dependent. Then, the direct involvement of amino acids consumed in the formation of proteins and volatile compounds has recently been reevaluated. Indeed, studies have highlighted the key role of lipids in nitrogen regulation in S. cerevisiae and their involvement in the mechanism of cell death. New winemaking strategies using non-Saccharomyces yeast strains in co- or sequential fermentation improve nitrogen management. Indeed, recent studies show that non-Saccharomyces yeasts have significant and specific needs for nitrogen. Moreover, sluggish fermentation can occur when they are associated with S. cerevisiae, necessitating nitrogen addition. In this context, we will present the consequences of nitrogen addition, discussing the sources, time of addition, transcriptome changes, and effect on volatile compound composition.