Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity

Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.

Small Differences in SUC Gene Sequences Impact Saccharomyces cerevisiae Invertase Activity and Specificity toward Fructans with Different Chain Lengths

Saccharomyces cerevisiae (S. cerevisiae)invertase is encoded by a family of closely related SUC genes. To identify and understand the molecular basis for differences in substrate specificity, we examined 29 SUC alleles from industrialS. cerevisiaestrains and cloned alleles with small sequence differences into an invertase-negative strain. Our study showed that an F102Y substitution in Suc-enzymes lowers yeast invertase activity toward fructo-oligosaccharides (FOS) by 36% and the specificity factor by 43%. By contrast, an A409P substitution in Suc-enzymes resulted in an increased capacity of the yeast to hydrolyze FOS and Fibruline by 17 and 41%, respectively, likely because of a change in the loop conformation resulting in a wider active site. Bread dough fermentation experiments revealed that sucrose and fructan hydrolysis during fermentation is influenced by this natural variation in SUC sequences. Our research thus opens the door for the selection or engineering of yeasts and Suc-enzymes with specific activities that may ultimately allow controlling fructan hydrolysis.

Variability in yeast invertase activity determines the extent of fructan hydrolysis during wheat dough fermentation and final FODMAP levels in bread

Consumption of fructan-containing cereal products is considered beneficial for most people, but not for those suffering from irritable bowel syndrome (IBS), as they should avoid the consumption of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (acronym: FODMAP). Controlling fructan levels in cereal products is not trivial. However, controlling yeast invertase-mediated hydrolysis of fructan during dough fermentation might offer a handle to modulate fructan concentrations. In this work, the variability in invertase activity and substrate specificity in an extensive set of industrial Saccharomyces cerevisiae strains is investigated. Analysis showed a high variability in the capacity of these strains to hydrolyse sucrose and fructo-oligosaccharides. Industrial yeast strains with a high activity towards fructo-oligosaccharides efficiently reduced wheat grain fructans during dough fermentation to a final fructan level of 0.3% dm, whereas strains with a low invertase activity yielded fructan levels around 0.6% dm. The non-bakery strains produced lower levels of CO₂ in fermenting dough resulting in lower loaf volumes. However, CO₂ production and loaf volume could be increased by the addition of 3% glucose. In conclusion, this study shows that variation in yeast invertase activity and specificity can be used to modulate the fructan content in bread, allowing the production of low FODMAP breads, or alternatively, breads with a higher soluble dietary fibre content.

Exploiting heterozygosity in industrial yeasts to create new and improved baker's yeasts

The main aim of the work was to utilize heterozygosity of industrial yeast strains to construct new baker's yeast strains. Commercial baker's yeast strain ALKO 743, its more ethanol tolerant descendant ALKO 554 selected initially for growth over 300 generations in increasing ethanol concentrations in a glucose medium, and ALKO 3460 from an old domestic sour dough starter were used as starting strains. Isolated meiotic segregants of the strains were characterized genetically for sporulation ability and mating type, and the ploidy was determined physically. Heterozygosity of the segregant strains was estimated by a variety of molecular characterizations and fermentation and growth assays. The results showed wide heterozygosity and that the segregants were clustered into subgroups. This clustering was used for choosing distantly or closely related partners for strain construction crosses. Intrastrain hybrids made with segregants of ALKO 743 showed 16-24% hybrid vigour or heterosis. Interstrain hybrids with segregants of ALKO 743 and ALKO 3460 showed a wide variety of characteristics but also clear heterosis of 27-31% effects as assayed by lean and sugar dough raising. Distiller's yeast ALKO 554 turned out to be a diploid genetic segregant and not just a more ethanol tolerant mutant of the tetraploid parent strain ALKO 743.