Domestication signatures in the non-conventional yeast Lachancea cidri.

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.

A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples.

Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.

Gradual Correction of Pediatric Equinus Deformity.

Pediatric equinus is broadly defined as generalized limited dorsiflexion at the ankle joint. It may result from either congenital or acquired causes and exhibit varying characteristics such as flexible, rigid, or spastic types. It has been extensively studied in literature and is known to be associated with the pathological condition of the bone, soft tissue, or combined deformity. In children, rigid plantarflexed cases can be debilitating and prevent them from ambulating without pain, if at all. As this volume in Clinics has chapters on comprehensive pediatric examination and neuromuscular disorders, this article will focus on (non-neurologic equinus) and its treatment via conservative and surgical methods with an emphasis on gradual correction.

Aromatic Higher Alcohols in Wine: Implication on Aroma and Palate Attributes during Chardonnay Aging.

The higher alcohols 2-phenylethanol, tryptophol, and tyrosol are a group of yeast-derived compounds that have been shown to affect the aroma and flavour of fermented beverages. Five variants of the industrial wine strain AWRI796, previously isolated due to their elevated production of the 'rose-like aroma' compound 2-phenylethanol, were characterised during pilot-scale fermentation of a Chardonnay juice. We show that these variants not only increase the concentration of 2-phenylethanol but also modulate the formation of the higher alcohols tryptophol, tyrosol, and methionol, as well as other volatile sulfur compounds derived from methionine, highlighting the connections between yeast nitrogen and sulfur metabolism during fermentation. We also investigate the development of these compounds during wine storage, focusing on the sulfonation of tryptophol. Finally, the sensory properties of wines produced using these strains were quantified at two time points, unravelling differences produced by biologically modulating higher alcohols and the dynamic changes in wine flavour over aging.

Preliminary Study of Australian Pinot Noir Wines by Colour and Volatile Analyses, and the Pivot© Profile Method Using Wine Professionals.

The aim of this preliminary study was to identify potential colour components, volatile and sensory attributes that could discriminate Pinot noir wines from five Australian winegrowing regions (Adelaide Hills, Yarra Valley, Mornington Peninsula, Northern and Southern Tasmania). The sensory analysis consisted of the Pivot© Profile method that was performed by wine professionals. A headspace solid-phase microextraction-gas chromatography-mass spectrometry method was used to quantify multiple volatile compounds, while the Modified Somers method was used for colour characterisation. Analysis of data suggested ethyl decanoate, ethyl 2-methylpropanoate, ethyl 2-methylbutanoate, in addition to decanoic acid as important contributors to the discrimination between regions. Similarly, wine hue, chemical age indices, total anthocyanin, and (%) non-bleachable pigment also discriminated wines between regions. The sensory analysis showed that wines from Mornington Peninsula were associated with the 'red fruits' aroma, 'acidic', and 'astringency' palate descriptors, while those from Adelaide Hills were associated with the 'brown' colour attribute. This study indicates regionality is a strong driver of aroma typicity of wine.

Commercial Saccharomyces cerevisiae Yeast Strains Significantly Impact Shiraz Tannin and Polysaccharide Composition with Implications for Wine Colour and Astringency.

To gain knowledge on the role of Saccharomyces cerevisiae yeast strains (and their hybrids) on wine sensory properties, 10 commercially available yeast strains were selected on the basis of their widespread usage and/or novel properties and used to produce Shiraz wines. Significant differences were evident post-alcoholic fermentation and after 24 months of ageing with regards to the number of wine compositional variables, in particular the concentration of tannin and polysaccharide. Strain L2323 is known for its pectinolytic activity and yielded the highest concentration of both yeast- and grape-derived polysaccharides. Wines made with the mannoprotein-producing strain Uvaferm HPS (high levels of polysaccharides) did not have elevated concentrations of yeast-derived polysaccharides, despite this observation being made for corresponding model fermentations, suggesting that mannoprotein production or retention might be limited by the wine matrix. Wine tannin concentration showed a high level of variability between strains, with L2323 having the highest, and AWRI1503 the lowest concentration. Sensory analysis of the wines after 24 months ageing revealed significant differences between the yeast strains, but only the attributes opacity (visual colour) and astringency could be predicted by partial least squares regression using the wine compositional data. Notably, the astringency attribute was associated with higher concentrations of both tannin and polysaccharide, contrary to reports in the literature which suggested that polysaccharide exerts a moderating effect on astringency. The results confirm previous reports demonstrating that the choice of yeast strain represents an opportunity to shape wine style outcomes.

Volatile profile of reduced alcohol wines fermented with selected non-Saccharomyces yeasts under different aeration conditions.

Over the last decades there has been an increase in ethanol concentration in wine. High ethanol concentration may impact negatively wine flavor and can be associated with harmful effects on human health. In this study, we investigated a microbiological approach to reduce wine ethanol concentration, using three non-Saccharomyces yeast strains (Metschnikowia pulcherrima, Torulaspora delbrueckii and Zygosaccharomyces bailii) in sequential fermentations with S. cerevisiae under different aeration conditions. At the same time, we evaluated the volatile profile of the resulting reduced alcohol Chardonnay wines. Results showed that the non-Saccharomyces yeasts tested were able to reduce wine ethanol concentration when oxygen was provided. Compared to S. cerevisiae wines, ethanol reduction was 1.6% v/v, 0.9% v/v and 1.0% v/v for M. pulcherrima, T. delbrueckii and Z. bailii sequential fermentations, respectively. Under the conditions evaluated here, aeration did not affect acetic acid production for any of the non-Saccharomyces strains tested. Although aeration affected wine volatile profiles, this was depended on yeast strain. Thus, wines produced with M. pulcherrima under aeration of 0.05 volume of air per volume of culture per minute (VVM) showed excessive ethyl acetate content, while Z. bailli wines produced with 0.05 VVM aeration had increased concentrations of higher alcohols and volatile acids. Increased concentrations of these compounds over their sensory thresholds, are likely to impact negatively on wine sensory profile. Contrarily, all three non-Saccharomyces strains under 0.025 VVM aeration conditions produced wines with reduced ethanol concentration and acceptable chemical volatile profiles.

Inactivating Mutations in Irc7p Are Common in Wine Yeasts, Attenuating Carbon-Sulfur ß-Lyase Activity and Volatile Sulfur Compound Production.

During alcoholic fermentation of grape sugars, wine yeasts produce a range of secondary metabolites that play an important role in the aroma profile of wines. In this study, we have explored the ability of a large number of wine yeast strains to modulate wine aroma composition, focusing on the release of the "fruity" thiols 3-mercaptohexan-1-ol (3-MH) and 4-mercapto-4-methylpentan-2-one (4-MMP) from their respective cysteinylated nonvolatile precursors. The role of the yeast gene IRC7 in thiol release has been well established, and it has been shown that a 38-bp deletion found in many wine strains cause them to express a truncated version of Irc7p that does not possess cysteine-S-conjugate ß-lyase activity. In our data, we find that IRC7 allele length alone does not fully explain the capacity of a strain to release thiols. Screening of a large number of strains coupled with analysis of genomic sequence data allowed us to identify several previously undescribed single-nucleotide polymorphisms (SNPs) in IRC7 that, when coupled with allele length, more robustly explain the ability of a particular yeast strain to release thiols from their cysteinylated precursors. We also demonstrate that allelic variation of IRC7 not only affects the release of thiols but modulates the formation of negative volatile sulfur compounds from the amino acid cysteine. The results of this study provide winemakers with an improved understanding of the genetic determinants that affect wine aroma and flavor, which can be used to guide the choice of yeast strains that are fit for purpose.IMPORTANCE Volatile sulfur compounds contribute to wine aromas that may be considered pleasant, such as "tropical," "passionfruit," and "guava," as well as aromas that are considered undesirable, such as "rotten eggs," "onions," and "sewer." During fermentation, wine yeasts release some of these compounds from odorless precursor molecules, a process that is most efficient when performed by yeasts that express active forms of the protein Irc7p. We show that most wine yeasts carry mutations that reduce activity of this protein, affecting the formation of volatile sulfur compounds that impart both pleasant and unpleasant aromas. The results provide winemakers with guidance on the choice of yeasts that can emphasize or deemphasize this particular contribution to wine quality.

Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains.

Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of 'omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the 'low-alcohol' phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.

Error-prone protein synthesis in parasites with the smallest eukaryotic genome.

Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis. We find that most microsporidian synthetases lack regulatory and eukaryote-specific appended domains and have a high degree of sequence variability in tRNA-binding and catalytic domains. In one synthetase, LeuRS, an apparent sequence degeneration annihilates the editing domain, a catalytic center responsible for the accurate selection of leucine for protein synthesis. Unlike accurate LeuRS synthetases from other eukaryotic species, microsporidian LeuRS is error-prone: apart from leucine, it occasionally uses its near-cognate substrates, such as norvaline, isoleucine, valine, and methionine. Mass spectrometry analysis of the microsporidium Vavraia culicis proteome reveals that nearly 6% of leucine residues are erroneously replaced by other amino acids. This remarkably high frequency of mistranslation is not limited to leucine codons and appears to be a general property of protein synthesis in microsporidian parasites. Taken together, our findings reveal that the microsporidian protein synthesis machinery is editing-deficient, and that the proteome of microsporidian parasites is more diverse than would be anticipated based on their genome sequences.

Novel wine yeast with ARO4 and TYR1 mutations that overproduce 'floral' aroma compounds 2-phenylethanol and 2-phenylethyl acetate.

It is well established that the choice of yeast used to perform wine fermentation significantly influences the sensory attributes of wines; different yeast species and strains impart different profiles of esters, volatile fatty acids, higher alcohols, and volatile sulphur compounds. Indeed, choice of yeast remains one of the simplest means by which winemakers can modulate the sensory characteristics of wine. Consequently, there are more than 100 commercially available Saccharomyces cerevisiae wine yeast strains available, mostly derived by isolation from vineyards and successful fermentations. Nevertheless, some desirable characteristics such as 'rose' and 'floral' aromas in wine are not present amongst existing strains. Such aromas can be conferred from the higher alcohol 2-phenylethanol (2-PE) and its acetate ester, 2-phenylethyl acetate (2-PEA). These metabolites of the aromatic amino acid phenylalanine are present at concentrations below their aroma detection thresholds in many wines, so their contribution to wine style is often minimal. To increase the concentration of phenylalanine metabolites, natural and chemically mutagenised populations of a S. cerevisiae wine strain, AWRI796, were exposed to toxic analogues of phenylalanine. Resistant colonies were found to overproduce 2-PE and 2-PEA by up to 20-fold, which resulted in a significant increase in 'floral' aroma in pilot-scale white wines. Genome sequencing of these newly developed strains revealed mutations in two genes of the biosynthetic pathway of aromatic amino acids, ARO4 and TYR1, which were demonstrated to be responsible for the 2-PE overproduction phenotype.

Transcriptional and post-transcriptional regulation of Cdc20 during the spindle assembly checkpoint in S. cerevisiae.

The anaphase-promoting complex (APC) is a ubiquitin ligase responsible for promoting the degradation of many cell cycle regulators. One of the activators and substrate-binding proteins for the APC is Cdc20. It has been shown previously that Cdc20 can promote its own degradation by the APC in normal cycling cells mainly through a cis-degradation mode (i.e. via an intramolecular mechanism). However, how Cdc20 is degraded during the spindle assembly checkpoint (SAC) is still not fully clear. In this study, we used a dual-Cdc20 system to investigate this issue and found that the cis-degradation mode is also the major pathway responsible for Cdc20 degradation during the SAC. In addition, we found that there is an inverse relationship between APCCdc20 activity and the transcriptional activity of the CDC20 promoter, which likely occurs through feedback regulation by APCCdc20 substrates, such as the cyclins Clb2 and Clb5. These findings contribute to our understanding of how the inhibition of APCCdc20 activity and enhanced Cdc20 degradation are required for proper spindle checkpoint arrest.