Saccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant Scale

Abstract

Saccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns previously revealed genes that underlie cellular adaptation to the grape must and wine environments, involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage, similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions.IMPORTANCE This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain undercharacterized, indicating the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.

Keywords: Saccharomyces cerevisiae; fermentation; gene expression.

FIG 1

California vineyard locations and fermentation patterns. (A) Map displaying the six AVAs in which the 10 study vineyards are located. (B) Fermentation curves reflecting the change in Brix over fermentation. Brix is a measure of total soluble solids that is used as a proxy for sugar concentration in grapes, grape must, and wine. (C) Brix at the time of sampling for each RNA-seq sample, relative to inoculation. While samples were taken at the same absolute time, fermentations proceeded at different rates, leading to different Brix values in each fermentation.

FIG 2

Transcriptome remodeling in fermentation is consistent across fermentations and vintages. (A) Graphs (y axis, normalized log gene expression counts; x axis, decrease in Brix over time) showing gene expression patterns in the 2017 and 2019 vintages, involving genes more highly expressed early (HXT1) and late (HXT4) in fermentation or constitutively (ADH1) across fermentation. (B) Upset plot showing the intersection of genes that are more highly expressed at the beginning and end of fermentation in each vintage, using a log₂ fold change cutoff value of 1. The majority of genes are consistently expressed across fermentations and vintages. (C) Proteomaps depicting Gene Ontology pathways (left) and genes (right) that are more highly expressed in early (top) and late (bottom) fermentation. The sizes of individual genes reflect the associated log₂ fold change values. Note that, for presentation purposes, not all genes that are significantly expressed are depicted. See Data Set S1 in the supplemental material for a complete list of genes.

FIG 3

Pathways enriched among genes differentially expressed across fermentation that are shared with the ESR. (A) Of 16 genes that overlap the ESR and are expressed in early fermentation, pathways related to carbohydrate metabolism were enriched. (B) Of 78 genes that overlap the ESR and are expressed later in fermentation, pathways related to oxidation-reduction and carbohydrate metabolism were enriched. GeneRatio refers to the fraction of genes in an enriched gene set that were present in the tested set.

FIG 4

Normalized log gene expression counts for genes involved in mannitol transport and degradation. HXT13 (A and C) and MAN2 (B and D) expression in the 2017 (A and B) and 2019 (C and D) vintages is graphed. MAN2 and HXT13 were the most-expressed genes at the end of fermentation in 2019 and fell behind only HXT4 in the 2017 vintage. Gray lines indicate a linear model fit to normalized counts.