Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing.

Acetic acid tolerance of the yeast Saccharomyces cerevisiae is manifested in several quantifiable parameters, of which the duration of the latency phase is one of the most studied. It has been shown recently that the latter parameter is mostly determined by a fraction of cells within the population that resumes proliferation upon exposure to acetic acid. The aim of the current study was to identify genetic determinants of the difference in this parameter between the highly tolerant strain MUCL 11987-9 and the laboratory strain CEN.PK113-7D. To this end, a combination of genetic mapping and pooled-segregant RNA sequencing was applied as a new approach. The genetic mapping data revealed four loci with a strong linkage to strain MUCL 11987-9, each containing still a large number of genes making the identification of the causal ones by traditional methods a laborious task. The genes were therefore prioritized by pooled-segregant RNA sequencing, which resulted in the identification of six genes within the identified loci showing differential expression. The relevance of the prioritized genes for the phenotype was verified by reciprocal hemizygosity analysis. Our data revealed the genes ESP1 and MET22 as two, so far unknown, genetic determinants of the size of the fraction of cells resuming proliferation upon exposure to acetic acid.

A new laboratory evolution approach to select for constitutive acetic acid tolerance in Saccharomyces cerevisiae and identification of causal mutations.

BACKGROUND: Acetic acid, released during hydrolysis of lignocellulosic feedstocks for second generation bioethanol production, inhibits yeast growth and alcoholic fermentation. Yeast biomass generated in a propagation step that precedes ethanol production should therefore express a high and constitutive level of acetic acid tolerance before introduction into lignocellulosic hydrolysates. However, earlier laboratory evolution strategies for increasing acetic acid tolerance of Saccharomyces cerevisiae, based on prolonged cultivation in the presence of acetic acid, selected for inducible rather than constitutive tolerance to this inhibitor. RESULTS: Preadaptation in the presence of acetic acid was shown to strongly increase the fraction of yeast cells that could initiate growth in the presence of this inhibitor. Serial microaerobic batch cultivation, with alternating transfers to fresh medium with and without acetic acid, yielded evolved S. cerevisiae cultures with constitutive acetic acid tolerance. Single-cell lines isolated from five such evolution experiments after 50-55 transfers were selected for further study. An additional constitutively acetic acid tolerant mutant was selected after UV-mutagenesis. All six mutants showed an increased fraction of growing cells upon a transfer from a non-stressed condition to a medium containing acetic acid. Whole-genome sequencing identified six genes that contained (different) mutations in multiple acetic acid-tolerant mutants. Haploid segregation studies and expression of the mutant alleles in the unevolved ancestor strain identified causal mutations for the acquired acetic acid tolerance in four genes (ASG1, ADH3, SKS1 and GIS4). Effects of the mutations in ASG1, ADH3 and SKS1 on acetic acid tolerance were additive. CONCLUSIONS: A novel laboratory evolution strategy based on alternating cultivation cycles in the presence and absence of acetic acid conferred a selective advantage to constitutively acetic acid-tolerant mutants and may be applicable for selection of constitutive tolerance to other stressors. Mutations in four genes (ASG1, ADH3, SKS1 and GIS4) were identified as causative for acetic acid tolerance. The laboratory evolution strategy as well as the identified mutations can contribute to improving acetic acid tolerance in industrial yeast strains.

The fraction of cells that resume growth after acetic acid addition is a strain-dependent parameter of acetic acid tolerance in Saccharomyces cerevisiae.

High acetic acid tolerance of Saccharomyces cerevisiae is a relevant phenotype in industrial biotechnology when using lignocellulosic hydrolysates as feedstock. A screening of 38 S. cerevisiae strains for tolerance to acetic acid revealed considerable differences, particularly with regard to the duration of the latency phase. To understand how this phenotype is quantitatively manifested, four strains exhibiting significant differences were studied in more detail. Our data show that the duration of the latency phase is primarily determined by the fraction of cells within the population that resume growth. Only this fraction contributed to the exponential growth observed after the latency phase, while all other cells persisted in a viable but non-proliferating state. A remarkable variation in the size of the fraction was observed among the tested strains differing by several orders of magnitude. In fact, only 11 out of 10(7)  cells of the industrial bioethanol production strain Ethanol Red resumed growth after exposure to 157 mM acetic acid at pH 4.5, while this fraction was 3.6 × 10(6) (out of 10(7)  cells) in the highly acetic acid tolerant isolate ATCC 96581. These strain-specific differences are genetically determined and represent a valuable starting point to identify genetic targets for future strain improvement.

Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation.

BACKGROUND: n-Butanol and isobutanol produced from biomass-derived sugars are promising renewable transport fuels and solvents. Saccharomyces cerevisiae has been engineered for butanol production, but its high butanol sensitivity poses an upper limit to product titers that can be reached by further pathway engineering. A better understanding of the molecular basis of butanol stress and tolerance of S. cerevisiae is important for achieving improved tolerance. RESULTS: By combining a screening of the haploid S. cerevisiae knock-out library, gene overexpression, and genome analysis of evolutionary engineered n-butanol-tolerant strains, we established that protein degradation plays an essential role in tolerance. Strains deleted in genes involved in the ubiquitin-proteasome system and in vacuolar degradation of damaged proteins showed hypersensitivity to n-butanol. Overexpression of YLR224W, encoding the subunit responsible for the recognition of damaged proteins of an ubiquitin ligase complex, resulted in a strain with a higher n-butanol tolerance. Two independently evolved n-butanol-tolerant strains carried different mutations in both RPN4 and RTG1, which encode transcription factors involved in the expression of proteasome and peroxisomal genes, respectively. Introduction of these mutated alleles in the reference strain increased butanol tolerance, confirming their relevance in the higher tolerance phenotype. The evolved strains, in addition to n-butanol, were also more tolerant to 2-butanol, isobutanol and 1-propanol, indicating a common molecular basis for sensitivity and tolerance to C3 and C4 alcohols. CONCLUSIONS: This study shows that maintenance of protein integrity plays an essential role in butanol tolerance and demonstrates new promising targets to engineer S. cerevisiae for improved tolerance.

A new methodology to obtain wine yeast strains overproducing mannoproteins.

Yeast mannoproteins are highly glycosylated proteins that are covalently bound to the beta-1,3-glucan present in the yeast cell wall. Among their outstanding enological properties, yeast mannoproteins contribute to several aspects of wine quality by protecting against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The development of a non-recombinant method to obtain enological yeast strains overproducing mannoproteins would therefore be very useful. Our previous experience on the genetic determinants of the release of these molecules by Saccharomyces cerevisiae has allowed us to propose a new methodology to isolate and characterize wine yeast that overproduce mannoproteins. The described methodology is based on the resistance of the killer 9 toxin produced by Williopsis saturnus, a feature linked to an altered biogenesis of the yeast cell wall.

Construction of a recombinant autolytic wine yeast strain overexpressing the csc1-1 allele.

During the aging step of sparkling wines and wines aged on lees, yeast cells kept in contact with the wine finally die and undergo autolysis, releasing cellular compounds with a positive effect on the wine quality. In view of the interest of autolysis for wine properties, biotechnologists have tried to improve autolytic yield during winemaking. In this work we used genetic engineering techniques to construct an autolytic industrial strain by expressing the csc1-1 allele from the RDN1 locus. The expression of this mutant allele, that causes a "constitutive in autophagy phenotype," resulted in accelerated autolysis of the recombinant strain. Although autophagic phenotype due to csc1-1 expression has been reported to require the mutant allele in multicopy, autolytic acceleration was achieved by expressing only one or two copies of the gene under the control of the constitutive promotor pTDH3. The acceleration of autolysis together with the unaltered fermentative capacity, strongly supported the overexpression of csc1-1 allele as a strategy to obtain wines with aged-like properties in a shortened time.

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.

A recombinant Saccharomyces cerevisiae strain overproducing mannoproteins stabilizes wine against protein haze.

Stabilization against protein haze was one of the first positive properties attributed to yeast mannoproteins in winemaking. In previous work we demonstrated that deletion of KNR4 leads to increased mannoprotein release in laboratory Saccharomyces cerevisiae strains. We have now constructed strains with KNR4 deleted in two different industrial wine yeast backgrounds. This required replacement of two and three alleles of KNR4 for the EC1118 and T73-4 backgrounds, respectively, and the use of three different selection markers for yeast genetic transformation. The actual effect of the genetic modification was dependent on both the genetic background and the culture conditions. The fermentation performance of T73-4 derivatives was clearly impaired, and these derivatives did not contribute to the protein stability of the wine, even though they showed increased mannoprotein release in vitro. In contrast, the EC1118 derivative with both alleles of KNR4 deleted released increased amounts of mannoproteins both in vitro and during wine fermentation assays, and the resulting wines were consistently less susceptible to protein haze. The fermentation performance of this strain was slightly impaired, but only with must with a very high sugar content. These results pave the way for the development of new commercial strains with the potential to improve several mannoprotein-related quality and technological parameters of wine.

Transgenic wine yeast technology comes of age: is it time for transgenic wine?

Saccharomyces cerevisiae is the main yeast responsible for alcoholic fermentation of grape juice during wine making. This makes wine strains of this species perfect targets for the improvement of wine technology and quality. Progress in winemaking has been achieved through the use of selected yeast strains, as well as genetic improvement of wine yeast strains through the sexual and pararexual cycles, random mutagenesis and genetic engineering. Development of genetically engineered wine yeasts, their potential application, and factors affecting their commercial viability will be discussed in this review.

Genetic determinants of the release of mannoproteins of enological interest by Saccharomyces cerevisiae.

Cell wall mannoproteins released by Saccharomyces cerevisiae during wine fermentation and aging have recently attracted the attention of enologists and researchers in enology due to their positive effect over a number of technological and quality properties of the wines, including protein and tartaric stability, aroma and color stability, astringency, mouthfeel, malolactic fermentation, or foam properties of sparkling wines. This work has investigated the effect of deletions involving genes related to cell wall biogenesis on the release of mannoproteins, as well as the effect of the released mannoproteins on wine protein stability. When available, the phenotypes have been studied in different genetic backgrounds, in haploid or diploid strains, and in homo- or heterozygosis. Strains deleted for GAS1, GPI7, or KNR4 release higher amounts of mannoproteins and polysaccharides to the medium. These increased amounts of mannoproteins and polysaccharides lead to a stronger stability of Sauvignon Blanc wines against protein haze.