Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

The dynamics of loss of heterozygosity events in genomes

Genomic instability is a hallmark of tumorigenesis, yet it also plays an essential role in evolution. Large-scale population genomics studies have highlighted the importance of loss of heterozygosity (LOH) events, which have long been overlooked in the context of genetic diversity and instability. Among various types of genomic mutations, LOH events are the most common and affect a larger portion of the genome. They typically arise from recombination-mediated repair of double-strand breaks (DSBs) or from lesions that are processed into DSBs. LOH events are critical drivers of genetic diversity, enabling rapid phenotypic variation and contributing to tumorigenesis. Understanding the accumulation of LOH, along with its underlying mechanisms, distribution, and phenotypic consequences, is therefore crucial. In this review, we explore the spectrum of LOH events, their mechanisms, and their impact on fitness and phenotype, drawing insights from Saccharomyces cerevisiae to cancer. We also emphasize the role of LOH in genomic instability, disease, and genome evolution.

Irc20 modulates LOH frequency and distribution in S. cerevisiae

Loss of Heterozygosity (LOH) due to mitotic recombination is frequently associated with the development of various cancers (e.g. retinoblastoma). LOH is also an important source of genetic diversity, especially in organisms where meiosis is infrequent. Irc20 is a putative helicase, and E3 ubiquitin ligase involved in DNA double-strand break repair pathway. We analyzed genome-wide LOH events, gross chromosomal changes, small insertion-deletions and single nucleotide mutations in eleven S. cerevisiae mutation accumulation lines of irc20∆, which underwent 50 mitotic bottlenecks. LOH enhancement in irc20∆ was small (1.6 fold), but statistically significant as compared to the wild type. Short (≤ 1 kb) and long (> 10 kb) LOH tracts were significantly enhanced in irc20∆. Both interstitial and terminal LOH events were also significantly enhanced in irc20∆ compared to the wild type. LOH events in irc20∆ were more telomere proximal and away from centromeres compared to the wild type. Gross chromosomal changes, single nucleotide mutations and in-dels were comparable between irc20∆ and wild type. Locus based and genome-wide analysis of meiotic recombination showed that meiotic crossover frequencies are not altered in irc20∆. These results suggest Irc20 primarily regulates mitotic recombination and does not affect meiotic crossovers. Our results suggest that the IRC20 gene is important for regulating LOH frequency and distribution.

Upper Bound on the Mutational Burden Imposed by a CRISPR-Cas9 Gene-Drive Element

CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, useful for eradication of disease vectors, conservation of endangered species and other applications. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to loss of heterozygosity (LOH). These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To estimate how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. Despite its substantial statistical power, our experiment revealed no detectable effect of CCGD or Cas9 alone on the genome-wide rates of mutations or LOH events, suggesting that these rates are affected by less than 30%. Nevertheless, we found that Cas9 caused a slight but significant shift towards more interstitial and fewer terminal LOH events, and the CCGD caused a significant difference in the distribution of LOH events on Chromosome V. Taken together, our results show that these genetic elements impose a weak and likely localized additional mutational burden in the yeast model. Although the mutagenic effects of CCGDs need to be further evaluated in other systems, our results suggest that the effect of CCGDs on off-target mutation rates and genetic diversity may be acceptable.

Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast

The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.

Loss of Heterozygosity and Its Importance in Evolution

Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.

Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate

BACKGROUND

Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids.

RESULTS

The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µ_max) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µ_max between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL.

CONCLUSIONS

The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.

Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae

Former studies have established that loss of heterozygosity can be a key driver of sequence evolution in unicellular eukaryotes and tissues of metazoans. However, little is known about whether the distribution of loss of heterozygosity events is largely random or forms discernible patterns across genomes. To initiate our experiments, we introduced selectable markers to both arms of all chromosomes of the budding yeast. Subsequent extensive assays, repeated over several genetic backgrounds and environments, provided a wealth of information on the genetic and environmental determinants of loss of heterozygosity. Three findings stand out. First, the number of loss of heterozygosity events per unit time was more than 25 times higher for growing than starving cells. Second, loss of heterozygosity was most frequent when regions of homology around a recombination site were identical, about a half-% sequence divergence was sufficient to reduce its incidence. Finally, the density of loss of heterozygosity events was highly dependent on the genome's physical architecture. It was several-fold higher on short chromosomal arms than on long ones. Comparably large differences were seen within a single arm where regions close to a centromere were visibly less affected than regions close, though usually not strictly adjacent, to a telomere. We suggest that the observed uneven distribution of loss of heterozygosity events could have been caused not only by an uneven density of initial DNA damages. Location-depended differences in the mode of DNA repair, or its effect on fitness, were likely to operate as well.

Intraspecific Variation in the Rates of Mutations Causing Structural Variation in Daphnia magna

Mutations that cause structural variation are important sources of genetic variation upon which other evolutionary forces can act, however, they are difficult to observe and therefore few direct estimates of their rate and spectrum are available. Understanding mutation rate evolution, however, requires adding to the limited number of species for which direct estimates are available, quantifying levels of intraspecific variation in mutation rates, and assessing whether rate estimates co-vary across types of mutation. Here, we report structural variation-causing mutation rates (svcMRs) for six categories of mutations (short insertions and deletions, long deletions and duplications, and deletions and duplications at copy number variable sites) from nine genotypes of Daphnia magna collected from three populations in Finland, Germany, and Israel using a mutation accumulation approach. Based on whole-genome sequence data and validated using simulations, we find svcMRs are high (two orders of magnitude higher than base substitution mutation rates measured in the same lineages), highly variable among populations, and uncorrelated across categories of mutation. Furthermore, to assess the impact of scvMRs on the genome, we calculated rates while adjusting for the lengths of events and ran simulations to determine if the mutations occur in genic regions more or less frequently than expected by chance. Our results pose a challenge to most prevailing theories aimed at explaining the evolution of the mutation rate, underscoring the importance of obtaining additional mutation rate estimates in more genotypes, for more types of mutation, in more species, in order to improve our future understanding of mutation rates, their variation, and their evolution.

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.

The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi

Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.

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.