Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation

Directed evolution as an approach to increase fructose utilization in synthetic grape juice by wine yeast AWRI 796

In winemaking, slow or stuck alcoholic fermentation can impact processing efficiency and wine quality. Residual fructose in the later stages of fermentation can leave the wine 'out of specification' unless removed, which requires reinoculation or use of a more fructophilic yeast. As such, robust, fermentation efficient strains are still highly desirable to reduce this risk. We report on a combined EMS mutagenesis and Directed Evolution (DE) approach as a 'proof of concept' to improve fructose utilization and decrease fermentation duration. One evolved isolate, Tee 9, was evaluated against the parent, AWRI 796 in defined medium (CDGJM) and Semillon juice. Interestingly, Tee 9 exhibited improved fermentation in CDGJM at several nitrogen contents, but not in juice. Genomic comparison between AWRI 796 and Tee 9 identified 371 mutations, but no chromosomal copy number variation. A total of 95 noncoding and 276 coding mutations were identified in 297 genes (180 of which encode proteins with one or more substitutions). Whilst introduction of two of these, Gid7 (E726K) or Fba1 (G135S), into AWRI 796 did not lead to the fermentation improvement seen in Tee 9, similar allelic swaps with the other mutations are needed to understand Tee 9's adaption to CDGJM. Furthermore, the 378 isolates, potentially mutagenized but with the same genetic background, are likely a useful resource for future phenotyping and genome-wide association studies.

CRISPR/Cas9-mediated Inactivation of arginase in a yeast strain isolated from Nuruk and its impact on the whole genome

Despite the advantages of CRISPR/Cas9 technology in the food industry, controversy over its off-target effects exists. We engineered an industrial Saccharomyces cerevisiae strain isolated from a Korean rice wine starter, Nuruk, using CRISPR/Cas9 to decrease ethyl carbamate (EC) formation. We disrupted the CAR1 gene encoding arginase, which plays a key role in EC formation. Subsequently, we compared the whole genome of the engineered strain to that of the wild type by analyzing heterozygous and homozygous mutations through variant calling. Homozygous mutations in the genome of the engineered strains were identified as the target mutations in CAR1 induced by CRISPR/Cas9, and no other off-target effects were observed. Our findings have critical implications for the use of CRISRP/Cas9 technology in yeasts in the food industry.

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.

Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts

Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.

Genome-Wide Analysis of Mitotic Recombination in Budding Yeast

DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides the repair reaction by using a homologous DNA template. The budding yeast Saccharomyces cerevisiae is an excellent model system with which to study this repair mechanism and the resulting patterns of genomic change resulting from it. In this chapter, we describe an approach that utilizes whole-genome sequencing data to support the analysis of tracts of loss-of-heterozygosity (LOH) that can arise from mitotic recombination in the context of the entire diploid yeast genome. The workflow and the discussion in this chapter are intended to enable classically trained molecular biologists and geneticists with limited experience in computational methods to conceptually understand and execute the steps of genome-wide LOH analysis as well as to adapt and apply them to their own specific studies and experimental models.

Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells

Genomic alterations including single-base mutations, deletions and duplications, translocations, mitotic recombination events, and chromosome aneuploidy generate genetic diversity. We examined the rates of all of these genetic changes in a diploid strain of Saccharomyces cerevisiae by whole-genome sequencing of many independent isolates (n = 93) subcloned about 100 times in unstressed growth conditions. The most common alterations were point mutations and small (<100 bp) insertion/deletions (n = 1,337) and mitotic recombination events (n = 1,215). The diploid cells of most eukaryotes are heterozygous for many single-nucleotide polymorphisms (SNPs). During mitotic cell divisions, recombination can produce derivatives of these cells that have become homozygous for the polymorphisms, termed loss-of-heterozygosity (LOH) events. LOH events can change the phenotype of the cells and contribute to tumor formation in humans. We observed two types of LOH events: interstitial events (conversions) resulting in a short LOH tract (usually less than 15 kb) and terminal events (mostly cross-overs) in which the LOH tract extends to the end of the chromosome. These two types of LOH events had different distributions, suggesting that they may have initiated by different mechanisms. Based on our results, we present a method of calculating the probability of an LOH event for individual SNPs located throughout the genome. We also identified several hotspots for chromosomal rearrangements (large deletions and duplications). Our results provide insights into the relative importance of different types of genetic alterations produced during vegetative growth.

Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids

Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S. uvarum hybrids preferentially retained S. uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.