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Wine cellar in the Agronomy and Viticulture Experimentation Unit at the INRA center in Colmar. Opening of a cask used in a microvinification experiment. © INRA, MAITRE Christophe

Yeast: how wines get made

The genes specific to wine yeasts

A few thousand years ago, winemaking yeast strains acquired genes coding for small-peptide transporters from a different yeast species. These genes provide a selective advantage in the grape-must environment. 

By Pascale Mollier, translated by Jessica Pearce
Updated on 12/23/2016
Published on 09/28/2016

Wine yeast strains belong to the species Saccharomyces cerevisiae, which exhibits a large degree of diversity and is found in very different ecological environments and geographic locations all over the world. Certain yeasts specialize in fermentation and are used to produce wine, sake, rum, beer, bread, and cheese. Others are found in nature, on trees and fruit.

A major scientific challenge has been to identify which parts of the genome help wine yeasts adapt to their local environments. Such knowledge should help researchers clarify the mechanisms underlying strain evolution and help focus artificial selection to obtain desirable traits.

Wine yeasts possess three genomic regions acquired via horizontal transfer

INRA researchers (3) compared the genomic sequences of two S. cerevisiae strains; one was a commercially available winemaking yeast (1) and the other was a laboratory yeast (2).  They discovered there were three regions unique to the wine yeast. Furthermore, these three regions were common in wine yeasts but scarce or absent from other strains, regardless of their fermentation abilities (e.g., sake versus oak yeasts; see sidebar). It would seem that wine yeasts acquired this genetic material from very distant relatives via horizontal transfer (4).

Certain genes result in selective advantages for wine yeasts

The researchers focused on one of the three regions because it contained some genes of interest. Of the twenty or so genes in the 65-kilobase region, they identified two genes in the FOT family. FOT genes encode peptide transporters (5) and were described in fungi by CNRS researchers in Lyon. “Peptide transporters likely play a role in fermentation, which involves both carbon and nitrogen metabolism,” explains INRA researcher Virginie Galeote. INRA scientists carried out an experiment in which they staged a competition in grape must between two versions of the same yeast strain: one with and one without the FOT genes.

. © INRA
. © INRA
. © INRA
. © INRA
Start of experiment End of 1st fermentation End of 2nd fermentation End of 3rd fermentation

Figure legend: Competition between two versions of the same yeast strain. One carried FOT genes (green fluorescent label) and the other did not (red label). The flow cytometry images depict the results of three successive fermentation cycles carried out in natural Chardonnay grape must.

Galeote comments, “The results were amazingly clear. Over three fermentation cycles, the strain with FOT genes competitively excluded the strain without FOT genes.” This experiment is the first in which horizontally transferred genes have been found to confer a selective advantage to wine yeasts.

FOT genes promote yeast growth, fermentation efficiency, and aroma formation

Armed with FOT genes, yeasts can transport a broader range of the peptides present in grape must, resulting in a greater exploitation of protein resources. Consequently, yeast growth, viability, and fermentation efficiency increase. Moreover, yeast metabolism is modified—more, desirable aromatic compounds are generated (6) and less acetate is produced. High concentrations of the latter compound are undesirable. Galeote continues, “We are now looking to characterize the peptides present in natural grape must. More specifically, we wish to identify those targeted by FOT transporters. Our preliminary research has found that grape must contains abundant glutamic acid, a peptide that serves as a key metabolic intermediary. This fact could explain how FOT genes enhance aroma formation.”

These results highlight how horizontal gene transfer can positively affect genome evolution and allow wine yeasts to adapt to environmental conditions.

(1) Strain sequenced in 2009.

(2) Non-fermenting strain sequenced in 1996.

(3) Sciences for Oenology Joint Research Unit, INRA center of Montpellier

(4) Horizontal gene transfer contrasts with vertical gene transfer, which is the product of genetic crossing within species. The mechanisms behind horizontal transfers remain poorly understood.

(5) Peptides: short chains of amino acids; amino acids are made up of a core carbon atom attached to amine and carboxylic acid groups as well as a specific side-chain.

(6) These results have implications for other INRA research, which has shown that aroma formation can be optimized by adjusting nitrogen concentration during fermentation (see article 5 of this report on yeasts and wine aroma).

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Marsit S., Mena A., Bigey F., Sauvage FX., Couloux A., Guy J., Legras JL., Barrio E., Dequin S., Galeote V. 2015. Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts. Mol Biol Evol. 32(7):1695-1707.

Damon C., Vallon L., Zimmermann ZHaider M.Z., Galeote V., Dequin S., Luis P., Fraissinet-Tachet L., and Marmeisse R. 2011. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J, 5:1871-1880.

Marsit S, Sanchez I, Galeote V, Dequin S. 2016. Horizontally acquired oligopeptide transporters favor adaptation of Saccharomyces cerevisiae wine yeast to enological environment. Environ. Microbiol. 18:1148-61.

Novo M., Bigey F., Beyne E., Galeote V., Gavory F., Mallet S., Cambon B., Legras J.L., Wincker P., Casaregola S. and Dequin S. 2009. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast S. cerevisiae EC1118. Proc. Nat. Acad. Sc. USA 106: 16333-16338.

Comparing the genomes of 58 yeast strains

Genome sequencing was carried out on 58 Saccharomyces cerevisiae strains. Representatives were chosen from a variety of ecological niches: for example, non-fermenting oak yeasts versus fermenting wine, sake, rum, beer, bread, and cheese yeasts. Genome comparisons highlighted that the three genomic regions mentioned above are largely specific to wine yeasts. However, they also showed that other horizontal transfers have taken place over the course of evolution, some of which appear to be group specific. Further analyses of the transferred genes should reveal their functions and the way in which they help yeasts adapt to specific ecological niches. Such research should also reveal more about strain origin. We already know that wine yeasts came from yeasts found on Mediterranean oaks and that sake yeasts are more closely related to yeasts found on US oaks (see article 3 of this report).