1. Introduction
Icewine is a signature sweet dessert wine that is fermented from the juice of naturally frozen grapes. Since much of the water in the grape is frozen at harvest, the pressed Icewine juice is highly concentrated in solutes such as sugars, organic acids, and nitrogenous compounds. For Icewine juice produced in the Niagara Peninsula of Ontario, Canada, the average sugar concentration for Vidal Icewine juice was reported at 39.3 Brix for 298 Icewine juice samples (approximately 450 g/L sugar) [
1]. The high sugar concentration presents a significant osmotic stress for the fermenting
Saccharomyces cerevisiae. High osmotic stress, commonly referred to as hyperosmotic stress, causes prolonged fermentation times, less than ideal alcohol yields, reduced biomass growth, and elevated levels of undesired metabolites [
2,
3]. The undesired metabolites, namely acetate, acetaldehyde, and ethyl acetate, indirectly arise because of the increased synthesis of glycerol, the primary compound responsible for the adaptation to hyperosmotic stress [
4]. Synthesis of glycerol is a two-step process that involves the reduction and dephosphorylation of the glycolytic intermediate, dihydroxyacetone phosphate (DHAP). Glycerol synthesis is not redox neutral, as one equivalent of NADH (nicotinamide adenine dinucleotide (NAD
+) + hydrogen (H)) is required per synthesized glycerol, resulting in the production of NAD
+ [
5,
6]. Therefore, a second reaction is required to reduce the generated NAD
+ back to NADH. The NADH generating step of glycolysis, the oxidation of glyceraldehyde 3-phosphate by glyceraldehyde 3-phosphate dehydrogenase, is balanced by coupling this step to alcoholic fermentation, where acetaldehyde is reduced to ethanol by alcohol dehydrogenase, regenerating NAD
+ and making this a redox neutral process. Excess oxidation of NADH through glycerol synthesis can lead to a significant shift in the NAD
+/NADH ratio [
7]. Due to the importance of NADH for the reduction of acetaldehyde to ethanol, reduced levels of NADH relative to NAD
+ causes insufficient acetaldehyde reduction, thus leading to elevated levels of acetaldehyde, and subsequently acetate, due to acetaldehyde oxidation by aldehyde dehydrogenases [
7,
8,
9].
In addition to glycerol synthesis, yeast can also actively uptake glycerol from the extracellular environment [
10]. One such transporter, Stl1p, is a plasma membrane H
+/glycerol symporter. The proton-glycerol symport mechanism of Stl1p allows for extracellular glycerol to be imported against a concentration gradient, at the cost of H
+ influx into the cell [
11]. As the name
STL (
sugar
transporter
like) suggests, the protein is one of 34 sugar permeases in yeast and is part of the major facilitator superfamily (MFS) [
12]. In laboratory yeast strains of
S. cerevisiae,
STL1 is reported as upregulated by salt-induced osmotic stress and repressed and inactivated by glucose, but glucose repression was overcome at high temperatures [
11,
13]. Previous gene expression analysis on the short-term hyperosmotic stress response in wine yeast to grape must inoculation revealed that
STL1 was highly expressed between the first 10 and 30 minutes, before rapid downregulation to near undetectable levels [
14]. Another gene expression analysis study found that
STL1 expression upregulation was very low in
S. cerevisiae wine yeast throughout table wine fermentations and in glucose-containing stress conditions [
15]. Conversely, we have previously reported that
STL1 is the most highly upregulated gene in
S. cerevisiae K1-V1116 during osmotically challenging Icewine fermentations, with a 25-fold increase relative to that measured in table wine fermentation being seen on the fifth day of fermentation [
16].
While gene expression analysis is a useful tool for identifying potential gene targets associated with a given phenotype, further investigation is often required to confirm protein function and phenotypic impact. Genetic modification is one such tool that can be used for gene function elucidation. Given the hyperosmotic conditions of Icewine, and the differences between laboratory yeast strains and wine yeast strains, constructing engineered wine yeast strains would be optimal for studying Icewine hyperosmotic stress condition responses [
17,
18,
19]. While
S. cerevisiae is amendable with existing genome editing techniques, primarily through the chromosomal integration of selectable markers in haploid auxotrophic strains, applying these techniques to industrially relevant diploid and polyploid strains, like wine yeasts, can be challenging and time-consuming [
20,
21]. Luckily, with the advent of CRISPR-Cas9 genome editing methods, yeast strain engineering has become rapid, efficient, and multiplexed [
22,
23]. At the time of this work, there has only been one other published study on the use of CRISPR-Cas9 for genome editing in wine yeasts. The work of Vigentini et al. (2017) used a double plasmid CRISPR-Cas9 method to eliminate
CAN1, an arginine permease, in the popular wine yeast strains, EC-1118 and AWR1796, thus lowering urea production [
24].
In this work, we developed a rapid and effective CRISPR-Cas9 genome editing method for the wine yeast S. cerevisiae strain, K1-V1116, which is commonly used for Icewine production. Using a single linearized CRISPR-Cas9 plasmid, that is repaired in vivo with a linear DNA fragment containing the target sequence of the sgRNA, we were able to construct a K1-V1116 strain featuring the complete removal of the STL1 open reading frame. Subsequent Icewine fermentations were conducted with K1-V1116 and K1-V1116 ∆STL1 strain. The reduced fermentation performance, along with increased glycerol and acetic acid production per gram of sugar consumed, of the ∆STL1 strain, provides further evidence that Stl1p contributes to the osmotolerance of K1-V1116 during Icewine fermentations, despite the high concentration of glucose.
2. Materials and Methods
2.1. Yeast Strains and Media
The commercial wine yeast used in this work was S. cerevisiae K1-V1116 (Lallemand, Montreal, QC, Canada). K1-V1116 strains were propagated using YPD (0.5% (w/v) Yeast Extract, 1% (w/v) Peptone, and 2% (w/v) Dextrose), unless otherwise stated. For solid media, 1% (w/v) agar was added. For selection media geneticin (G418) (Teknova, Hollister, CA, USA) was supplemented on YPD plates at 200 µg mL−1.
2.2. Description of CRISPR-Cas9 Method
The CRISPR-Cas9 method used in this work was built upon the work by the Tom Ellis lab [
25]. The plasmid used, pWS173, contains cassettes for the yeast expression of both Cas9 and sgRNA (
Figure 1). The yeast-optimized Cas9 contains a nuclear localization sequence and is driven by the PGK1 promoter. The optimized sgRNA cassette contains a yeast tRNA and 5’ HDV ribozyme and is flanked by 500 bp junk DNA homology arms. In pWS173, the sgRNA cassette contains a BsmBI-flanked GFP dropout for the 20 bp protospacer sequence required for targeted endonuclease activity. The method relies on the repair of a BsmBI linearized pWS173 with a 1.1 kb linear DNA fragment, which has the sgRNA cassette, with a 20 bp protospacer sequence, inserted within. The sgRNA repair DNA is generated using pWS173 as a template, with two PCR amplicons containing primer overhangs that encode for the protospacer sequence and the terminal sequence of the adjacent fragment. The two protospacer encoding amplicons are then assembled using overlap extension PCR, as described in
Section 2.3. When the linearized plasmid, sgRNA repair DNA, and donor DNA are transformed into yeast, the homology arms on the sgRNA repair DNA and pWS173 are recognized and the plasmid is circularized (
Figure 2a). The circularization of the plasmid restores its functionality, offering G418 resistance and expression of CRISPR-Cas9 and the active sgRNA species (
Figure 2b).
2.3. Cloning
The plasmid used in this work, pWS173, was a gift from Tom Ellis (Addgene plasmid # 90960). Plasmids were propagated in
NEB Stable™ Competent Escherichia coli (New England Biolabs), under the selection of LB (1% (
w/
v) Tryptone, 0.5% (
w/
v) Yeast Extract, 1% (
w/
v) Sodium Chloride) supplemented with 50 µg mL
−1 kanamycin (Tocris Biosciences, Bristol, UK). The plasmid was isolated using QIAprep Spin Miniprep (Qiagen, Hilden, Germany), linearized using BsmBI (New England Biolands, Ipswich, MA, USA) and used without gel extraction. The sequences from EC-1118 [
26] were used in place of K1-V1116 for all construct and primer design purposes, since the sequence of EC-1118 was available on the Ensembl genome browser. Benchling (San Francisco, CA, USA) was used for plasmid and construct design. The target sequence for CRISPR-Cas9 sgRNA, used in K1-V1116, was designed using the Benchling CRISPR tool, with the default parameters for the NGG PAM single guide RNA for Cas9. The R64-1-1
S. cerevisiae reference genome was used for off-target analysis. The target sequence used can be found in
Table A1. Donor DNA and sgRNA repair DNA was synthesized using 2-part overlap extension PCR, using Q5 polymerase (New England Biolands, Ipswich, MA, USA) and the primers in
Table A2. An initial annealing temperature of 55 °C was used for most PCR reactions, with the temperature adjusted empirically to resolve low yield reactions. An extension time of 15 second per kb and 35 cycles was used for all PCRs. For overlap extension PCR, 0.5 µL of the PCR mix each fragment was used as templates in a 50 µL reaction. Genomic DNA was isolated and purified from K1-V1116 using the Fungi/Yeast Genomic DNA Isolation Kit (Norgen Biotek, Thorold, ON, Canada). PCR amplified DNA was purified using QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). DNA was quantified using a NanoDrop Lite Spectrophotometer (ThermoFisher, Waltham, MA, USA). PCR amplicons were visualized using 1% agarose-TAE (40 mM Tris, 20 mM acetate, and 1 mM EDTA), containing 0.003% (
v/
v) RedSafe nucleic acid staining solution (iNtRON Biotechnology, Seongnam, Korea).
2.4. Strain Construction
The
S. cerevisiae strain, K1-V1116, was transformed using a modified electroporation protocol, which was largely based off the protocol described by DiCarlo et al. (2013) [
27]. A colony of K1-V1116 was inoculated into 5.5 mL of YPD. The culture was then incubated overnight at 30 °C in a roller drum. The following day, the culture was centrifuged at 8000 G for 1 min in a microcentrifuge. The media was removed, and the pellets were resuspended in 250 µL of room-temperature water and consolidated into a single tube. The cells were washed twice more, using 1 mL of water, and then resuspended in 1.5 mL of 500 mM lithium acetate with 5 mM of dithiothreitol (DTT) before being incubated for 30 min at 30 °C in a roller drum. Following conditioning, the cells were collected by centrifugation and washed twice with 1.5 mL of ice-cold electroporation buffer (1 M sorbitol and 1 mM calcium chloride). The final cell pellet was then resuspended in 950 µL of ice-cold electroporation buffer and kept on ice. For each transformation, 100 µL of cells were mixed with linearized pWS173 plasmid, sgRNA repair DNA, and donor DNA. The mixture was then transferred to an ice cold 0.2 cm gap electroporation cuvette and electroporated at 2.5 kV, 25 µF, and 200 Ω. The electroporated cells were recovered in 900 µL of room-temperature recovery media (0.5 M sorbitol and 0.5x YPD) and incubated for 4 h at 30 °C in a roller drum. After recovery, 50 µL of culture was plated onto YPD, supplemented with 200 µg mL
−1 G418 (geneticin) and incubated at 30 °C for 24 to 48 h. The remaining recovered culture was saved at 4 °C and plated again if required. Integration events were confirmed with colony PCR using Q5 polymerase (New England Biolabs, Ipswich, MA, USA). To obtain colony PCR DNA, a single colony was mixed into 25 µL of 20 mM sodium hydroxide and boiled at 90 °C for 10 min. PCR products were visualized using agarose gel electrophoresis, as described in
Section 2.2.
2.5. Icewine Juice
Vidal Icewine juice was previously acquired from Huebel Grape Estates in Niagara-on-the-Lake, Ontario, Canada and stored at −35 °C until use. The Icewine juice was thawed at 7 °C for 24 h, before being racked off and filtered through a series of coarse, medium, and fine pore size pad filters using the Bueno Vino Mini Jet filter (Vineco, St. Catharines, ON, Canada). The juice was then filter sterilized using 0.45 µm membrane cartridge (Millipore, Etobicoke, ON, Canada). The final sterile filtered Icewine juice (40.2 Brix) was used for Icewine fermentations. The sterile filtered Icewine juice contained 447 g L−1 sugar, pH 3.79, titratable acidity of 7.0 g L−1 tartaric acid, glycerol at 8.67 g L−1, acetic acid at 0.06 g L−1 and yeast assimilable nitrogen (YAN) at 441 mg N L−1.
2.6. Permissive Condition Growth Kinetics Characterization
Permissive condition growth kinetics characterization was conducted aerobically in YPD liquid media at 30 °C in an orbital shaker. In a sterile bottle with a stir bar, 250 mL of YPD was added, along with 450 mg of yeast cells from an agar plate, for each strain. This culture was stirred for 5 min on a stir plate and then was sampled into 75 mL aliquots in 250 mL Erlenmeyer flasks with sponge stoppers. The flasks were then placed in an orbital incubator set to 120 RPM and 30° C, and were sampled every two hours. Optical density at 600 nm (OD600) values were obtained using a Genesys 10S UV-Vis Spectrometer (Thermo Scientific, Waltham, MA, USA) set to 600 nm in absorbance mode, with methacrylate cuvettes. Dilutions were made with sterile YPD as needed, to stay under a reading of 1.0. All readings were done in triplicate.
2.7. Icewine Fermentations and Samplings
The K1-V1116 strains used for fermentations were prepared as starter cultures. The starter culture consisted of filter sterilized Icewine juice diluted to 10 Brix, with an additional 2 g L−1 of diammonium phosphate (DAP). From YPD plates, four freshly cultured yeast colonies were collected and used to inoculate 100 mL of starter culture media. The culture was incubated until the cell concentration reached 2 × 108 cells mL−1, or approximately 17 h, using a shaker table incubator set to 30 °C.
The starter culture was used to inoculate 1 L of Icewine juice to a final cell density of approximately 1 × 107 cells mL−1. The fermentations were incubated at 17 °C for 34 days. Samples were taken every day between days 0 and 6, every other day between days 8 and 16, and every three days between days 19 and 34. Before sampling, the fermentations were stirred for 5 min to ensure homogeneity, after which 2 mL of the culture was taken. After centrifugation, the supernatant of the sample was transferred to a clean tube and stored at −35 °C for later metabolite analysis. The remaining cell pellet was used for total and viable cell counts using methylene blue on a hemocytometer. Larger 50 mL samples were taken from the initial juice and final wine and stored at −35 °C for later analysis. Colony PCR was conducted on the strains at the beginning and end of fermentation to verify the genotype. The fermentations were conducted in triplicate for each strain.
2.8. Metabolite Analysis
Soluble solids were determined by ABBE bench top refractometer (model 10450; American Optical, Buffalo, NY, USA). Acidity was determined by pH measurement using a sympHony pH meter (model B10P; VWR, Mississauga, ON, Canada), and titratable acidity by titration against 0.1 mol L
−1 NaOH, to an endpoint of pH 8.2 [
28]. Glucose, fructose, glycerol, acetic acid, amino nitrogen, and ammonia nitrogen were measured using Megazyme assay kits (K-FRUGL, K-ACET, K-GCROL, K-PANOPA, K-AMIAR; Megazyme International Ireland, Ltd., Bray, Co. Wicklow, Ireland). Ethanol was determined by gas chromatography (Model 6890; Agilent Technologies Inc., Palo Alto, CA, USA) equipped with a flame ionization detector (FID), split/split-less injector, and Chemstation software (version E.02.00.493). Separations were carried out with a DB
®-WAX (30 m, 0.25 mm, 0.25 μm) GC column (122-7032 model; Agilent Technologies, Santa Clara, CA, USA) with helium as the carrier gas, at a flow rate of 1.5 mL min
−1. Metabolite production during fermentation was calculated by the difference in the respective metabolite concentration measured between the time zero point (immediately after inoculation) and at each sampling time point throughout fermentations. Normalized metabolite production was determined by dividing the final metabolite production by the final sugar consumed.
2.9. Statistical Analysis
XLSTAT-Pro by Addinsoft (New York, NY, USA) was used for statistical analysis. Analysis of variance (ANOVA) with mean separation by Tukey’s Honest Significant Difference (p < 0.05) and Student’s t-Test (p < 0.05, p < 0.01, p < 0.001) were used to evaluate differences between variables.
4. Discussion
The CRISPR-Cas9 genome editing method developed was effective in modifying the commercial wine yeast strain, K1-V1116, with various protocol optimization strategies. The use of a single plasmid which contains all required elements, except for the protospacer sequence, in conjunction with overlap extension PCR generated sgRNA repair DNA, allows for rapid testing of other loci. While the use of primers and in vitro DNA assembly can lead to mutations, the resulting 1.1 kb sgRNA repair DNA can be rapidly sequenced with Sanger sequencing. Alternatively, commonly used sgRNA repair DNA fragments could be cloned into an E. coli vector for sequence verification and maintenance. The use of overlap extension PCR to generate the ∆STL1 donor DNA was fitting for an edit which is not sensitive to single-nucleotide polymorphisms and indels, but such a cloning method is not appropriate for a sequence sensitive edit, like a gene overexpression cassette. Future work that ventures into sensitive edit types will need to rely on other high-fidelity and verifiable cloning methods.
The initial antibiotic resistance testing of K1-V1116 demonstrated that the strain is no more resistant than previously used strains. We believe the rapid test was sufficient, as notable background growth was not encountered for the remaining transformations. The initial transformation trials, with various K1-V1116 cultures as the source for electrocompetent cells, reinforced the previous findings that use of stationary phase cells was many orders of magnitude less efficient than log phase cells [
29,
30]. For the isogenic goal of this work, the use of stationary phase yeast for electroporation resulted in acceptable transformation efficiencies and greatly reduced the work required for transformation. Whether future work utilizes stationary phase cells will depend on the goal of the project. Conveniently, the use of the repaired pWS173 and sgRNA repair DNA appears to be more effective than a larger circularized plasmid. This observation indicates that the homologous recombination in K1-V1116 is active and potentially comparable to that of many laboratory
S. cerevisiae strains [
31]. The editing efficiency seen with the ∆
STL1 edit, 84%, was high enough for practical uses, and is within the ranges seen across many CRISPR-Cas9 methods [
22].
The Icewine fermentation trials conducted with K1-V1116 ∆
STL1 demonstrated the serious consequences that removing the Stl1p transporter has on fermentation performance. The sluggish fermentation, as indicated by the drastically reduced sugar consumption and total cell count, indicates that cell growth was inhibited by the deletion. The higher level of normalized glycerol production suggests that, since glycerol uptake is disrupted, the cell has an increased reliance on endogenous glycerol synthesis to satisfy demand under the hyperosmotic conditions. With the increased glycerol production per sugar consumed, the normalized acetic acid levels increased as well. Given the current understanding of glycerol synthesis and the NAD
+/NADH ratio during Icewine fermentations, the increased glycerol demand correlates with higher acetic acid levels [
4,
8,
16]. The exact cause of the reduced fermentation performance still needs to be determined. The increased demand on glycerol synthesis may further increase the NAD
+/NADH ratio and disrupt the metabolic flux of the many reactions which rely on NAD
+/NADH [
32,
33]. The inability to meet the glycerol demand could result in cell shrinkage, thus leading to the crowding of macromolecules and the slowing of cellular processes [
34]. The accumulation of the toxic fermentation intermediate, acetaldehyde, may also contribute to the sluggish fermentation [
35]. The exact cause of this phenomenon appears to not be acutely toxic to the cells, as the viable cell concentration of K1-V1116 ∆
STL1 was relatively stable throughout stationary phase. The maintained viability, despite the reduced performance, is not abnormal for other known causes of sluggish fermentations [
36].
These results, in conjunction with previous findings that
STL1 was the most highly upregulated gene during Icewine fermentations, strongly suggest that Stl1p has a role in maintaining internal glycerol levels during the hyperosmotic stress conditions of an Icewine fermentation [
4,
16]. The previous studies on
STL1 expression reveal that expression is low when glucose is present, even in the relatively stressful environments of table wine fermentations [
11,
13,
14,
15]. Our findings are similar to recent gene expression analysis research in sugarcane bioethanol strains, which showed that
STL1 glucose repression was overcome in 30 and 35 °Brix conditions [
37]. Future work should investigate whether overcoming glucose repression and inactivation at high sugar concentrations is a shared attribute between strains, or if certain strains have evolved the ability to overcome it. Considering many other yeast species rely on glycerol uptake to satisfy osmotic stress glycerol demand, it appears natural for
S. cerevisiae strains like K1-V1116 to rely more on glycerol uptake during hyperosmotic stress conditions [
38,
39]. Furthermore, the role of initial glycerol levels in Icewine juice needs to be determined, as reduced starting glycerol levels may negatively impact the effectiveness of Stl1p-mediated osmotolerance.