Engineering Saccharomyces cerevisiae for targeted hydrolysis and fermentation of glucuronoxylan through CRISPR/Cas9 genome editing.

BACKGROUND: The abundance of glucuronoxylan (GX) in agricultural and forestry residual side streams positions it as a promising feedstock for microbial conversion into valuable compounds. By engineering strains of the widely employed cell factory Saccharomyces cerevisiae with the ability to directly hydrolyze and ferment GX polymers, we can avoid the need for harsh chemical pretreatments and costly enzymatic hydrolysis steps prior to fermentation. However, for an economically viable bioproduction process, the engineered strains must efficiently express and secrete enzymes that act in synergy to hydrolyze the targeted polymers. RESULTS: The aim of this study was to equip the xylose-fermenting S. cerevisiae strain CEN.PK XXX with xylanolytic enzymes targeting beechwood GX. Using a targeted enzyme approach, we matched hydrolytic enzyme activities to the chemical features of the GX substrate and determined that besides endo-1,4-ß-xylanase and ß-xylosidase activities, α-methyl-glucuronidase activity was of great importance for GX hydrolysis and yeast growth. We also created a library of strains expressing different combinations of enzymes, and screened for yeast strains that could express and secrete the enzymes and metabolize the GX hydrolysis products efficiently. While strains engineered with BmXyn11A xylanase and XylA ß-xylosidase could grow relatively well in beechwood GX, strains further engineered with Agu115 α-methyl-glucuronidase did not display an additional growth benefit, likely due to inefficient expression and secretion of this enzyme. Co-cultures of strains expressing complementary enzymes as well as external enzyme supplementation boosted yeast growth and ethanol fermentation of GX, and ethanol titers reached a maximum of 1.33 g L- 1 after 48 h under oxygen limited condition in bioreactor fermentations. CONCLUSION: This work underscored the importance of identifying an optimal enzyme combination for successful engineering of S. cerevisiae strains that can hydrolyze and assimilate GX. The enzymes must exhibit high and balanced activities, be compatible with the yeast's expression and secretion system, and the nature of the hydrolysis products must be such that they can be taken up and metabolized by the yeast. The engineered strains, particularly when co-cultivated, display robust growth and fermentation of GX, and represent a significant step forward towards a sustainable and cost-effective bioprocessing of GX-rich biomass. They also provide valuable insights for future strain and process development targets.

Hybridization and spore dissection of native wine yeasts for improvement of ethanol resistance and osmotolerance.

Global warming has a significant impact on different viticultural parameters, including grape maturation. An increment of photosynthetic activity generates a rapid accumulation of sugars in the berry, followed by a dehydration process which leads to a higher concentration of soluble solids. This effect is exacerbated by current viticultural practices which favor the harvest of very mature grapes to obtain wines with sweet tannins. Considering the initial hyperosmotic stress conditions and the high ethanol concentration of the produced wine, fermentation of grape musts with high sugar content could be problematic for yeast starters. In the present study, we were able to obtain by classical hybridization and spore dissection methods one hybrid and one monosporic wine yeast strain with a combined ethanol and osmotolerant phenotype. The improved yeasts were tested in vinification trials with high sugar concentration and displayed excellent fermentation performance. Importantly, the obtained wines also showed good organoleptic properties during sensory analysis. Based on our results, we believed our improved hybrid and monosporic strains can be considered good alternatives to be used as yeast starters for fermentations with high sugar content.

Mutagenesis, screening and isolation of Brettanomyces bruxellensis mutants with reduced 4-ethylphenol production.

The use of non-conventional yeast species to obtain interesting flavors and aromas has become a new trend in the fermented beverages industry. Among such species, Brettanomyces bruxellensis (B. bruxellensis) has been reported as capable of producing desirable or at least singular aromas in fermented beverages like beer and wine. However, this yeast can also produce an aromatic defect by producing high concentrations of phenolic compounds like, 4-ethylguaiacol and particularly 4-ethylphenol (4-EP). In the present study, we designed a mutant screening method to isolate B. bruxellensis mutants with reduced 4-EP production. More than 1000 mutants were screened with our olfactory screening method, and after further sensory and chemical analysis we were able to select a B. bruxellensis mutant strain with a significant reduction of 4-EP production (more than threefold) and less phenolic perception. Notably, the selected strain also showed higher diversity and concentration of ethyl esters, the most important group of odor active compounds produced by yeasts. Based on these results, we consider that our selected mutant strain is a good candidate to be tested as a non-conventional yeast starter (pure or in co-inoculation) to obtain wines and beers with novel aromatic properties.

Generation of a Non-Transgenic Genetically Improved Yeast Strain for Wine Production from Nitrogen-Deficient Musts.

The yeast Saccharomyces cerevisiae is the main species responsible for the process that involves the transformation of grape must into wine, with the initial nitrogen in the grape must being vital for it. One of the main problems in the wine industry is the deficiency of nitrogen sources in the grape must, leading to stuck or sluggish fermentations, and generating economic losses. In this scenario, an alternative is the isolation or generation of yeast strains with low nitrogen requirements for fermentation. In the present study, we carry out a genetic improvement program using as a base population a group of 70 strains isolated from winemaking environments mainly in Chile and Argentina (F0), making from it a first and second filial generation (F1 and F2, respectively) based in different families and hybrids. It was found that the trait under study has a high heritability, obtaining in the F2 population strains that consume a minor proportion of the nitrogen sources present in the must. Among these improved strains, strain "686" specially showed a marked drop in the nitrogen consumption, without losing fermentative performance, in synthetic grape must at laboratory level. When using this improved strain to produce wine from a natural grape must (supplemented and non-supplemented with ammonium) at pilot scale under wine cellar conditions, a similar fermentative capacity was obtained between this strain and a widely used commercial strain (EC1118). However, when fermented in a non-supplemented must, improved strain "686" showed the presence of a marked floral aroma absent for EC1118 strain, this difference being probably a direct consequence of its different pattern in amino acid consumption. The combination of the capacity of improved strain "686" to ferment without nitrogen addition and produce floral aromas may be of commercial interest for the wine industry.

Construction of low-ethanol-wine yeasts through partial deletion of the Saccharomyces cerevisiae PDC2 gene.

We propose an alternative GMO based strategy to obtain Saccharomyces cerevisiae mutant strains with a slight reduction in their ability to produce ethanol, but with a moderate impact on the yeast metabolism. Through homologous recombination, two truncated Pdc2p proteins Pdc2pΔ344 and Pdc2pΔ519 were obtained and transformed into haploid and diploid lab yeast strains. In the pdc2Δ344 mutants the DNA-binding and transactivation site of the protein remain intact, whereas in pdc2Δ519 only the DNA-binding site is conserved. Compared to the control, the diploid BY4743pdc2Δ519 mutant strain reduced up to 7.4% the total ethanol content in lab scale-vinifications. The residual sugar and volatile acidity was not significantly affected by this ethanol reduction. Remarkably, we got a much higher ethanol reduction of 10 and 15% when the pdc2Δ519 mutation was tested in a native and a commercial wine yeast strain against their respective controls. Our results demonstrate that the insertion of the pdc2Δ519 mutation in wine yeast strains can reduce the ethanol concentration up to 1.89% (v/v) without affecting the fermentation performance. In contrast to non-GMO based strategies, our approach permits the insertion of the pdc2Δ519 mutation in any locally selected wine strain, making possible to produce quality wines with regional characteristics and lower alcohol content. Thus, we consider our work a valuable contribution to the problem of high ethanol concentration in wine.

Biodiversity of Saccharomyces cerevisiae populations in Malbec vineyards from the "Zona Alta del Río Mendoza" region in Argentina.

The "Zona Alta del Río Mendoza" (ZARM) is the major Malbec grape viticulture region of Argentina. The aim of the present study was to explore Saccharomyces cerevisiae biodiversity in ZARM vineyards. Interdelta PCR and RFLP mtDNA molecular markers were applied to differentiate S. cerevisiae strains. The presence of commercial strains on ZARM vineyards was also assessed. Our results reveal a highly diverse, but genetically closely related, S. cerevisiae population (containing more than 190 molecular patterns among 590 S. cerevisiae isolates). According to the S. cerevisiae strain diversity found in vineyards, they were classified as vineyards with high and low polymorphic S. cerevisiae populations. Six vineyards showed a high polymorphic population, with more than 20 different S. cerevisiae molecular patterns. S. cerevisiae populations in these vineyards were diverse and irregularly distributed, with different strains in each vineyard site. Low polymorphic S. cerevisiae population vineyards displayed very low yeast diversity, with only 9 to 10 different S. cerevisiae strains and presence of two commercial strains widely distributed. Population diversity estimators were calculated to determine the population structure of S. cerevisiae in the ZARM vineyards. The obtained values support the hypothesis that the eight sampled subpopulations come indeed from a larger population.

Cyk3 acts in actomyosin ring independent cytokinesis by recruiting Inn1 to the yeast bud neck.

Cytokinesis in yeast can be achieved by plasma membrane ingression, which is dependent on actomyosin ring constriction. Inn1 presumably couples these processes by interaction with both the plasma membrane and the temporary actomyosin ring component Hof1. In addition, an actomyosin ring independent cytokinesis pathway exists in yeast. We here identified Cyk3, a key component of the alternative pathway, as a novel interaction partner of Inn1. The carboxy-terminal proline rich part of Inn1 binds the SH3 domains of either Cyk3 or Hof1. Strains with truncated proteins lacking either of these SH3 domains do not display any severe phenotypes, but are synthetically lethal, demonstrating their crucial role in cytokinesis. Overexpression of CYK3 leads to an actomyosin ring independent recruitment of Inn1 to the bud neck, further supporting the significance of this interaction in vivo. Moreover, overexpression of CYK3 in a myo1 or an iqg1 deletion not only restores viability, but also the recruitment of Inn1 to the bud neck. We propose that Cyk3 is part of an actomyosin ring independent cytokinesis pathway, which acts as a rescue mechanism to recruit Inn1 to the bud neck.

Effect of partitioning equilibria on the activity of beta-galactosidase in heterogeneous media.

We had demonstrated that membrane adsorption or penetration differentially modulated beta-Galactosidase (beta-Gal) activity against soluble substrates (Coll. and Surf., 24, 21, 2002). In a heterogeneous media, not only the enzyme but also the rest of the chemical species taking part in a chemical reaction would eventually interact with the available surfaces. The aim of the present work was to investigate if, in addition to changes in the intrinsic mechanism of the reaction at the lipid-water interface, the kinetics of enzyme-catalyzed reactions could be significantly affected by the partitioning of the substrate (ortho-nitro-phenyl galactopyranoside (ONPG)), the product (ortho-nitro-phenol (ONP)) and the enzyme (E. coli beta-Gal) towards the membrane. Multilamellar vesicles of sPC were used as model membranes. Membrane-water partition coefficients (Pm/w) were determined according to the theory and methodology developed previously (J. Neurosci. Meth. 36, 203, 1991). The values of Pm/w obtained (PONPG =0, PONP =50 and P beta-Gal = 118) were applied to a two-compartment model, which assumed a free access of the substrate to the enzyme and a nucleophile-like activatory effect exerted, within the membrane compartment, by the lipid-water interface. This model: (i) reproduced the lipid concentration-dependence we had observed previously in Vmax, (ii) predicted the values of k4 = 3.54 x 10(7) s-1 and the extinction coefficient of the aglycone in the membrane phase, 4012 M(-1) cm-1, with p < 0.0001 and p < 0.02, respectively, as well as for P beta-Gal =117 (which was poor (p=0.6716) but gave a numerical value within the same order of magnitude that the experimental value) and (iii) emphasized the importance of the more efficient reaction mechanism in the membrane phase compared with that in the aqueous phase (k4>>k3).