Manuel Quirós

Selection of non-Saccharomyces yeast strains for reducing alcohol levels in wine by sugar respiration.

Respiration of sugars by non-Saccharomyces yeasts has been recently proposed for lowering alcohol levels in wine. Development of industrial fermentation processes based on such an approach requires, amongst other steps, the identification of yeast strains which are able to grow and respire under the relatively harsh conditions found in grape must. This work describes the characterization of a collection of non-Saccharomyces yeast strains in order to identify candidate yeast strains for this specific application. It involved the estimation of respiratory quotient (RQ) values under aerated conditions, at low pH and high sugar concentrations, calculation of yields of ethanol and other relevant metabolites, and characterization of growth responses to the main stress factors found during the first stages of alcoholic fermentation. Physiological features of some strains of Metschnikowia pulcherrima or two species of Kluyveromyces, suggest they are suitable for lowering ethanol yields by respiration. The unsuitability of Saccharomyces cerevisiae strains for this purpose was not due to ethanol yields (under aerated conditions they are low enough for a significant reduction in final ethanol content), but to the high acetic acid yields under these growth conditions. According to results from controlled aeration fermentations with one strain of M. pulcherrima, design of an aeration regime allowing for lowering ethanol yields though preserving grape must components from excessive oxidation, would be conceivable.

Metabolic Flux Analysis during the Exponential Growth Phase of Saccharomyces cerevisiae in Wine Fermentations

As a consequence of the increase in global average temperature, grapes with the adequate phenolic and aromatic maturity tend to be overripe by the time of harvest, resulting in increased sugar concentrations and imbalanced C/N ratios in fermenting musts. This fact sets obvious additional hurdles in the challenge of obtaining wines with reduced alcohols levels, a new trend in consumer demands. It would therefore be interesting to understand Saccharomyces cerevisiae physiology during the fermentation of must with these altered characteristics. The present study aims to determine the distribution of metabolic fluxes during the yeast exponential growth phase, when both carbon and nitrogen sources are in excess, using continuous cultures. Two different sugar concentrations were studied under two different winemaking temperature conditions. Although consumption and production rates for key metabolites were severely affected by the different experimental conditions studied, the general distribution of fluxes in central carbon metabolism was basically conserved in all cases. It was also observed that temperature and sugar concentration exerted a higher effect on the pentose phosphate pathway and glycerol formation than on glycolysis and ethanol production. Additionally, nitrogen uptake, both quantitatively and qualitatively, was strongly influenced by environmental conditions. This work provides the most complete stoichiometric model used for Metabolic Flux Analysis of S. cerevisiae in wine fermentations employed so far, including the synthesis and release of relevant aroma compounds and could be used in the design of optimal nitrogen supplementation of wine fermentations.

Three different targets for the genetic modification of wine yeast strains resulting in improved effectiveness of bentonite fining.

Bentonite fining is used in the clarification of white wines to prevent protein haze. This treatment results in the loss of a significant portion of the wine itself, as well as aroma compounds important for the quality of white wines. Among other interesting effects on wine quality, yeast cell wall mannoproteins have been shown to stabilize wine against protein haze. A previous work showed that wine yeast strains engineered by deletion of KNR4 release increased amounts of mannoproteins and produce wines showing attenuated responses in protein haze tests. This paper describes the technological properties of several new recombinant wine yeast strains, deleted for genes involved in cell-wall biogenesis, as well as the regulatory gene KNR4. Stabilization of wines produced by three of the six recombinant strains analyzed required 20-40% less bentonite than those made with their nonrecombinant counterparts. The availability of multiple targets for genetically improving yeast mannoprotein release, as shown in this work, is relevant not only for genetic engineering of wine yeast but especially for the feasibility of genetically improving this character by classical methods of strain development such as random mutagenesis or sexual hybridization.

Genome-wide study of the adaptation of Saccharomyces cerevisiae to the early stages of wine fermentation.

This work was designed to identify yeast cellular functions specifically affected by the stress factors predominating during the early stages of wine fermentation, and genes required for optimal growth under these conditions. The main experimental method was quantitative fitness analysis by means of competition experiments in continuous culture of whole genome barcoded yeast knockout collections. This methodology allowed the identification of haploinsufficient genes, and homozygous deletions resulting in growth impairment in synthetic must. However, genes identified as haploproficient, or homozygous deletions resulting in fitness advantage, were of little predictive power concerning optimal growth in this medium. The relevance of these functions for enological performance of yeast was assessed in batch cultures with single strains. Previous studies addressing yeast adaptation to winemaking conditions by quantitative fitness analysis were not specifically focused on the proliferative stages. In some instances our results highlight the importance of genes not previously linked to winemaking. In other cases they are complementary to those reported in previous studies concerning, for example, the relevance of some genes involved in vacuolar, peroxisomal, or ribosomal functions. Our results indicate that adaptation to the quickly changing growth conditions during grape must fermentation require the function of different gene sets in different moments of the process. Transport processes and glucose signaling seem to be negatively affected by the stress factors encountered by yeast in synthetic must. Vacuolar activity is important for continued growth during the transition to stationary phase. Finally, reduced biogenesis of peroxisomes also seems to be advantageous. However, in contrast to what was described for later stages, reduced protein synthesis is not advantageous for the early (proliferative) stages of the fermentation process. Finally, we found adenine and lysine to be in short supply for yeast growth in some natural grape musts.

An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must

We used experimental evolution in order to identify genes involved in the adaptation of Saccharomyces cerevisiae to the early stages of alcoholic fermentation. Evolution experiments were run for about 200 generations, in continuous culture conditions emulating the initial stages of wine fermentation. We performed whole-genome sequencing of four adapted strains from three independent evolution experiments. Mutations identified in these strains pointed to the Rsp5p-Bul1/2p ubiquitin ligase complex as the preferred evolutionary target under these experimental conditions. Rsp5p is a multifunctional enzyme able to ubiquitinate target proteins participating in different cellular processes, while Bul1p is an Rsp5p substrate adaptor specifically involved in the ubiquitin-dependent internalization of Gap1p and other plasma membrane permeases. While a loss-of-function mutation in BUL1 seems to be enough to confer a selective advantage under these assay conditions, this did not seem to be the case for RSP5 mutated strains, which required additional mutations, probably compensating for the detrimental effect of altered Rsp5p activity on essential cellular functions. The power of this experimental approach is illustrated by the identification of four independent mutants, each with a limited number of SNPs, affected within the same pathway. However, in order to obtain information relevant for a specific biotechnological process, caution must be taken in the choice of the background yeast genotype (as shown in this case for auxotrophies). In addition, the use of very stable continuous fermentation conditions might lead to the selection of a rather limited number of adaptive responses that would mask other possible targets for genetic improvement.

New insights into the advantages of ammonium as a winemaking nutrient.

Nitrogen limitation is the most common cause for stuck or sluggish fermentation in winemaking, and it is usually dealt with by supplementing grape juice with either ammonium salts or organic nutrients. These practices have a direct impact on both fermentation kinetics and the sensorial features of the final product. The aim of this work is to provide a detailed characterization of yeast physiology in response to ammonium supplementation during alcoholic fermentation. This is done by determining changes in metabolic rates on a high frequency basis, as a sensitive way to detect the impact of fermentation conditions on yeast physiology. Our results indicate that the choice of supplementation strategy has an impact on several enological parameters like fermentation length, volatile acidity, final glycerol content, and aroma profile. Interestingly, a higher proportion of ammonium relates with improved glycerol and volatile acidity, for the same global yeast assimilable nitrogen content. However, ammonium over-supplementation has a negative impact on quality related parameters, notably on volatile acidity and aroma complexity. Production kinetics and final content of several volatile compounds are also differentially influenced by standard or excess ammonium supplementation.

Identification of target genes to control acetate yield during aerobic fermentation with Saccharomyces cerevisiae

BackgroundAerobic fermentation of grape must, leading to respiro-fermentative metabolism of sugars, has been proposed as way of reducing alcohol content in wines. Two factors limit the usefulness of Saccharomyces cerevisiae for this application, the Crabtree effect, and excess volatile acidity under aerobic conditions. This work aimed to explore the impact on ethanol acetate production of different S. cerevisiae strains deleted for genes previously related with the Crabtree phenotype.ResultsRecombinant strains were constructed on a wine industrial genetic background, FX10. All yeast strains, including FX10, showed respiro-fermentative metabolism in natural grape must under aerobic conditions, as well as a concomitant reduction in ethanol yield. This indicates that the Crabtree effect is not a major constrain for reaching relevant respiration levels in grape must. Indeed, only minor differences in ethanol yield were observed between the original and some of the recombinant strains. In contrast, some yeast strains showed a relevant reduction of acetic acid production. This was identified as a positive feature for the feasibility of alcohol level reduction by respiration. Reduced acetic acid production was confirmed by a thorough analysis of these and some additional deletion strains (involving genes HXK2, PYK1, REG1, PDE2 and PDC1). Some recombinant yeasts showed altered production of glycerol and pyruvate derived metabolites.ConclusionsREG1 and PDC1 deletion strains showed a strong reduction of acetic acid yield in aerobic fermentations. Since REG1 defective strains may be obtained by non-GMO approaches, these gene modifications show good promise to help reducing ethanol content in wines.

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae

Adaptation to changes in osmolarity is fundamental for the survival of living cells, and has implications in food and industrial biotechnology. It has been extensively studied in the yeast Saccharomyces cerevisiae, where the Hog1 stress activated protein kinase was discovered about 20 years ago. Hog1 is the core of the intracellular signaling pathway that governs the adaptive response to osmotic stress in this species. The main endpoint of this program is synthesis and intracellular retention of glycerol, as a compatible osmolyte. Despite many details of the signaling pathways and yeast responses to osmotic challenges have already been described, genome-wide approaches are contributing to refine our knowledge of yeast adaptation to hypertonic media. In this work, we used a quantitative fitness analysis approach in order to deepen our understanding of the interplay between yeast cells and the osmotic environment. Genetic requirements for proper growth under osmotic stress showed both common and specific features when hypertonic conditions were induced by either glucose or sorbitol. Tolerance to high-glucose content requires mitochondrial function, while defective protein targeting to peroxisome, GID-complex function (involved in negative regulation of gluconeogenesis), or chromatin dynamics, result in poor survival to sorbitol-induced osmotic stress. On the other side, the competitive disadvantage of yeast strains defective in the endomembrane system is relieved by hypertonic conditions. This finding points to the Golgi-endosome system as one of the main cell components negatively affected by hyperosmolarity. Most of the biological processes highlighted in this analysis had not been previously related to osmotic stress but are probably relevant in an ecological and evolutionary context.

Genetic Improvement and Genetically Modified Microorganisms

Nowadays, any reflection about wine preferences and the impact of this important constituent of the Mediterranean diet on human health must take into account the current production context, which has extremely evolved during the last few decades. The number of technological advances with potential or hypothetical impact on wine quality as a whole is extremely diverse, and almost any novelty, agronomical, technological, or microbiological, raises arguments involving not only quality and safety considerations but also trade and ideological ones. Although only marginally affected, the winemaking industry has not totally escaped some controversy concerning the global debate on genetic engineering as a tool to improve yield and quality in the agro-food industry. In this chapter we focus on all methodologies historically developed for the genetic improvement of starter wine microorganisms, including not only the highly debated GMO techniques but a number of alternative genetic tools. These non-GMO alternatives often offer great technical advantages while avoiding the most controversial sides associated to genetic improvement. Indeed, some of them are actually undergoing an authentic revival. Both the basic principles behind these techniques and the improvement purposes currently pursued are treated in different sections. For the sake of brevity, and despite many initial advances in this field were fuelled by research on laboratory yeast strains, examples detailed in this chapter emphasise on research involving authentic winemaking yeast and bacterial strains or its direct derivatives. Marketing and regulatory considerations are extremely relevant in this field and are also discussed in the context of the current regulatory framework, trying to identify the most probable lines of development of these technologies in the near future, and their potential to reach the real wine market in the short or mid-term.