Genome-wide mapping of cellular traits using yeast

The search for Schizosaccharomyces fission yeasts in environmental meta-transcriptomes

Fission yeast is an important model organism in evolutionary genetics and cell biology research. Nevertheless, most research is limited to a single laboratory strain and knowledge of its natural occurrence is limited, which reduces our understanding of its life history and hinders isolation of new strains from nature. Understanding the natural diversity of fission yeast can provide insight into its genetic and phenotypic diversity and the evolutionary processes that shaped these. Here we aimed to identify candidate natural habitats of fission yeasts by searching through a large collection of publicly available environmental metatranscriptomic datasets. Using a custom pipeline, we processed over 13,000 NCBI SRA accessions, from a wide range of 34 different environmental categories. Overall, we found a very low abundance of putative yeast transcripts, with most fission yeast signatures coming from the categories of 'food' and 'terrestrial arthropods'. Additionally, a signal could be found in a variety of marine and fresh aquatic habitats. Our results do not provide a conclusive answer on the natural habitat of fission yeasts, but our analysis further narrows the range of locations where fission yeasts naturally occur.

Polygenic Analysis in Absence of Major Effector ATF1 Unveils Novel Components in Yeast Flavor Ester Biosynthesis

Flavor production in yeast fermentation is of paramount importance for industrial production of alcoholic beverages. Although major enzymes of flavor compound biosynthesis have been identified, few specific mutations responsible for strain diversity in flavor production are known. The ATF1-encoded alcohol acetyl coenzyme A (acetyl-CoA) transferase (AATase) is responsible for the majority of acetate ester biosynthesis, but other components affecting strain diversity remain unknown. We have performed parallel polygenic analysis of low production of ethyl acetate, a compound with an undesirable solvent-like off-flavor, in strains with and without deletion of ATF1 We identified two unique causative mutations, eat1^K179fs and snf8^E148*, not present in any other sequenced yeast strain and responsible for most ethyl acetate produced in absence of ATF1EAT1 encodes a putative mitochondrial ethanol acetyl-CoA transferase (EATase) and its overexpression, but not that of EAT1^K179fs , and strongly increases ethyl acetate without affecting other flavor acetate esters. Unexpectedly, a higher level of acetate esters (including ethyl acetate) was produced when eat1^K179fs was present together with ATF1 in the same strain, suggesting that the Eat1 and Atf1 enzymes are intertwined. On the other hand, introduction of snf8^E148* lowered ethyl acetate levels also in the presence of ATF1, and it affected other aroma compounds, growth, and fermentation as well. Engineering of snf8^E148* in three industrial yeast strains (for production of wine, saké, and ale beer) and fermentation in an application-relevant medium showed a high but strain-dependent potential for flavor enhancement. Our work has identified EAT1 and SNF8 as new genetic elements determining ethyl acetate production diversity in yeast strains.IMPORTANCE Basic research with laboratory strains of the yeast Saccharomyces cerevisiae has identified the structural genes of most metabolic enzymes, as well as genes encoding major regulators of metabolism. On the other hand, more recent work on polygenic analysis of yeast biodiversity in natural and industrial yeast strains is revealing novel components of yeast metabolism. A major example is the metabolism of flavor compounds, a particularly important property of industrial yeast strains used for the production of alcoholic beverages. In this work, we have performed polygenic analysis of production of ethyl acetate, an important off-flavor compound in beer and other alcoholic beverages. To increase the chances of identifying novel components, we have used in parallel a wild-type strain and a strain with a deletion of ATF1 encoding the main enzyme of acetate ester biosynthesis. This revealed a new structural gene, EAT1, encoding a putative mitochondrial enzyme, which was recently identified as an ethanol acetyl-CoA transferase in another yeast species. We also identified a novel regulatory gene, SNF8, which has not previously been linked to flavor production. Our results show that polygenic analysis of metabolic traits in the absence of major effector genes can reveal novel structural and regulatory genes. The mutant alleles identified can be used to affect the flavor profile in industrial yeast strains for production of alcoholic beverages in more subtle ways than by deletion or overexpression of the already known major effector genes and without significantly altering other industrially important traits. The effect of the novel variants was dependent on the genetic background, with a highly desirable outcome in the flavor profile of an ale brewing yeast.

Gene-gene and gene-environment interactions in complex traits in yeast

One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context-dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene-gene interactions (GGI) and gene-environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype-phenotype map.

The natural diversity and ecology of fission yeast

While the fission yeast is a powerful model of eukaryote biology, there have been few studies of quantitative genetics, phenotypic or genetic diversity. Here I survey the small collection of fission yeast diversity research. I discuss what we can infer about the ecology and origins of Schizosaccharomyces pombe from microbiology field studies and the few strains that have been collected.

Enhancing the performance of brewing yeasts

Beer production is one of the oldest known traditional biotechnological processes, but is nowadays facing increasing demands not only for enhanced product quality, but also for improved production economics. Targeted genetic modification of a yeast strain is one way to increase beer quality and to improve the economics of beer production. In this review we will present current knowledge on traditional approaches for improving brewing strains and for rational metabolic engineering. These research efforts will, in the near future, lead to the development of a wider range of industrial strains that should increase the diversity of commercial beers.

Mapping Quantitative Trait Loci in Yeast

Natural Saccharomyces strains isolated from the wild differ quantitatively in molecular and organismal phenotypes. Quantitative trait loci (QTL) mapping is a powerful approach for identifying sequence variants that alter gene function. In yeast, QTL mapping has been used in designed crosses to map functional polymorphisms. This approach, outlined here, is often the first step in understanding the molecular basis of quantitative traits. New large-scale sequencing surveys have the potential to directly associate genotypes with organismal phenotypes, providing a broader catalog of causative genetic variants. Additional analysis of intermediate phenotypes (e.g., RNA, protein, or metabolite levels) can produce a multilayered and integrated view of individual variation, producing a high-resolution view of the genotype-phenotype map.

Budding Yeast Strains and Genotype-Phenotype Mapping

A small number of well-studied laboratory strains of Saccharomyces cerevisiae, mostly derived from S288C, are used in yeast research. Although powerful, studies for understanding S288C do not always capture the phenotypic essence or the genetic complexity of S. cerevisiae biology. This is particularly problematic for multilocus phenotypes identified in laboratory strains because these loci have never been jointly exposed to natural selection and the corresponding phenotypes do not represent optimization for any particular purpose or environment. Isolation and sequencing of new natural yeast strains also reveal that the total sequence diversity of the S. cerevisiae global population is poorly sampled in common laboratory strains. Here we discuss methodologies required for using the natural genetic variation in yeast to complete a genotype-phenotype map.

The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae

Background

Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci.

Results

In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature. We detected four genomic regions involved in the adaptation at low temperature, three of them located in the subtelomeric regions (chromosomes XIII, XV and XVI) and one in the chromosome XIV. The QTL analysis revealed that subtelomeric regions play a key role in defining individual variation, which emphasizes the importance of these regions’ adaptive nature.

Conclusions

The reciprocal hemizygosity analysis (RHA), run to validate the genes involved in low-temperature fermentation, showed that genetic variation in mitochondrial proteins, maintenance of correct asymmetry and distribution of phospholipid in the plasma membrane are key determinants of low-temperature adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3572-2) contains supplementary material, which is available to authorized users.

RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast

Different natural yeast populations have faced dissimilar selective pressures due to the heterogeneous fermentation substrates available around the world; this increases the genetic and phenotypic diversity in Saccharomyces cerevisiae In this context, we expect prominent differences between isolates when exposed to a particular condition, such as wine or sake musts. To better comprehend the mechanisms underlying niche adaptation between two S. cerevisiae isolates obtained from wine and sake fermentation processes, we evaluated fermentative and fungicide resistance phenotypes and identify the molecular origin of such adaptive variation. Multiple regions were associated with fermentation rate under different nitrogen conditions and fungicide resistance, with a single QTL co-localizing in all traits. Analysis around this region identified RIM15 as the causative locus driving fungicide sensitivity, together with efficient nitrogen utilization and glycerol production in the wine strain. A null RIM15 variant confers a greater fermentation rate through the utilization of available glucose instead of its storage. However, this variant has a detrimental effect on fungicide resistance since complex sugars are not synthesized and transported into the membrane. Together, our results reveal the antagonist pleiotropic nature of a RIM15 null variant, positively affecting a series of fermentation related phenotypes, but apparently detrimental in the wild.

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype.

Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion

In somatic cells, recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events (LOH), allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection. However, inter-homolog recombination in somatic cells is rare, thus reducing potential genetic variation. Here, we explored the property of S. cerevisiae to enter the meiotic developmental program, induce meiotic Spo11-dependent double-strand breaks genome-wide and return to mitotic growth, a process known as Return To Growth (RTG). Whole genome sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid strain demonstrates that the RTGs are bona fide diploids with mosaic recombined genome, derived from either parental origin. Individual RTG genome-wide genotypes are comprised of 5 to 87 homozygous regions due to the loss of heterozygous (LOH) events of various lengths, varying between a few nucleotides up to several hundred kilobases. Furthermore, we show that reiteration of the RTG process shows incremental increases of homozygosity. Phenotype/genotype analysis of the RTG strains for the auxotrophic and arsenate resistance traits validates the potential of this procedure of genome diversification to rapidly map complex traits loci (QTLs) in diploid strains without undergoing sexual reproduction.

Yeast as a cell factory: current state and perspectives

The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used microorganisms in biotechnology with successful applications in the production of both bulk and fine chemicals. Yet, yeast researchers are faced with the challenge to further its transition from the old workhorse to a modern cell factory, fulfilling the requirements for next generation bioprocesses. Many of the principles and tools that are applied for this development originate from the field of synthetic biology and the engineered strains will indeed be synthetic organisms. We provide an overview of the most important aspects of this transition and highlight achievements in recent years as well as trends in which yeast currently lags behind. These aspects include: the enhancement of the substrate spectrum of yeast, with the focus on the efficient utilization of renewable feedstocks, the enhancement of the product spectrum through generation of independent circuits for the maintenance of redox balances and biosynthesis of common carbon building blocks, the requirement for accurate pathway control with improved genome editing and through orthogonal promoters, and improvement of the tolerance of yeast for specific stress conditions. The causative genetic elements for the required traits of the future yeast cell factories will be assembled into genetic modules for fast transfer between strains. These developments will benefit from progress in bio-computational methods, which allow for the integration of different kinds of data sets and algorithms, and from rapid advancement in genome editing, which will enable multiplexed targeted integration of whole heterologous pathways. The overall goal will be to provide a collection of modules and circuits that work independently and can be combined at will, depending on the individual conditions, and will result in an optimal synthetic host for a given production process.

Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test

The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.

Insights into molecular evolution from yeast genomics

Enabled by comparative genomics, yeasts have increasingly developed into a powerful model system for molecular evolution. Here we survey several areas in which yeast studies have made important contributions, including regulatory evolution, gene duplication and divergence, evolution of gene order and evolution of complexity. In each area we highlight key studies and findings based on techniques ranging from statistical analysis of large datasets to direct laboratory measurements of fitness. Future work will combine traditional evolutionary genetics analysis and experimental evolution with tools from systems biology to yield mechanistic insight into complex phenotypes.

Heritability and genetic basis of protein level variation in an outbred population

The genetic basis of heritable traits has been studied for decades. Although recent mapping efforts have elucidated genetic determinants of transcript levels, mapping of protein abundance has lagged. Here, we analyze levels of 4084 GFP-tagged yeast proteins in the progeny of a cross between a laboratory and a wild strain using flow cytometry and high-content microscopy. The genotype of trans variants contributed little to protein level variation between individual cells but explained >50% of the variance in the population’s average protein abundance for half of the GFP fusions tested. To map trans-acting factors responsible, we performed flow sorting and bulk segregant analysis of 25 proteins, finding a median of five protein quantitative trait loci (pQTLs) per GFP fusion. Further, we find that cis-acting variants predominate; the genotype of a gene and its surrounding region had a large effect on protein level six times more frequently than the rest of the genome combined. We present evidence for both shared and independent genetic control of transcript and protein abundance: More than half of the expression QTLs (eQTLs) contribute to changes in protein levels of regulated genes, but several pQTLs do not affect their cognate transcript levels. Allele replacements of genes known to underlie trans eQTL hotspots confirmed the correlation of effects on mRNA and protein levels. This study represents the first genome-scale measurement of genetic contribution to protein levels in single cells and populations, identifies more than a hundred trans pQTLs, and validates the propagation of effects associated with transcript variation to protein abundance.