Timing and Order of the Molecular Events Marking the Onset of Berry Ripening in Grapevine.

Grapevine (Vitis vinifera) is a model for the investigation of physiological and biochemical changes during the formation and ripening of nonclimacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/midripening, and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/midripening phase. Coexpression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.

Yeast alter micro-oxygenation of wine: oxygen consumption and aldehyde production.

BACKGROUND: Micro-oxygenation (MOx) is a common winemaking treatment used to improve red wine color development and diminish vegetal aroma, amongst other effects. It is commonly applied to wine immediately after yeast fermentation (phase 1) or later, during aging (phase 2). Although most winemakers avoid MOx during malolactic (ML) fermentation, it is often not possible to avoid because ML bacteria are often present during phase 1 MOx treatment. We investigated the effect of common yeast and bacteria on the outcome of micro-oxygenation. RESULTS: Compared to sterile filtered wine, Saccharomyces cerevisiae inoculation significantly increased oxygen consumption, keeping dissolved oxygen in wine below 30 µg L-1 during micro-oxygenation, whereas Oenococcus oeni inoculation was not associated with a significant impact on the concentration of dissolved oxygen. The unfiltered baseline wine also had both present, although with much higher populations of bacteria and consumed oxygen. The yeast-treated wine yielded much higher levels of acetaldehyde, rising from 4.3 to 29 mg L-1 during micro-oxygenation, whereas no significant difference was found between the bacteria-treated wine and the filtered control. The unfiltered wine exhibited rapid oxygen consumption but no additional acetaldehyde, as well as reduced pyruvate. Analysis of the acetaldehyde-glycerol acetal levels showed a good correlation with acetaldehyde concentrations. CONCLUSION: The production of acetaldehyde is a key outcome of MOx and it is dramatically increased in the presence of yeast, although it is possibly counteracted by the metabolism of O. oeni bacteria. Additional controlled experiments are necessary to clarify the interaction of yeast and bacteria during MOx treatments. Analysis of the glycerol acetals may be useful as a proxy for acetaldehyde levels. © 2017 Society of Chemical Industry.

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments.

Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this species--i.e., its "pan-genome"--has been less explored. We created a multispecies microarray platform containing probes covering the genomes of several Saccharomyces species: S. cerevisiae, including regions not found in the standard laboratory S288c strain, as well as the mitochondrial and 2-µm circle genomes-plus S. paradoxus, S. mikatae, S. kudriavzevii, S. uvarum, S. kluyveri, and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) on 83 different S. cerevisiae strains collected across a wide range of habitats; of these, 69 were commercial wine strains, while the remaining 14 were from a diverse set of other industrial and natural environments. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole-genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.

Comparative metabolic footprinting of a large number of commercial wine yeast strains in Chardonnay fermentations.

Wine has been made for thousands of years. In modern times, as the importance of yeast as an ingredient in winemaking became better appreciated, companies worldwide have collected and marketed specific yeast strains for enhancing positive and minimizing negative attributes in wine. It is generally believed that each yeast strain contributes uniquely to fermentation performance and wine style because of its genetic background; however, the impact of metabolic diversity among wine yeasts on aroma compound production has not been extensively studied. We characterized the metabolic footprints of 69 different commercial wine yeast strains in triplicate fermentations of identical Chardonnay juice, by measuring 29 primary and secondary metabolites; we additionally measured seven attributes of fermentation performance of these strains. We identified up to 1000-fold differences between strains for some of the metabolites and observed large differences in fermentation performance, suggesting significant metabolic diversity. These differences represent potential selective markers for the strains that may be important to the wine industry. Analysis of these metabolic traits further builds on the known genomic diversity of these strains and provides new insights into their genetic and metabolic relatedness.