Frequent ploidy changes in growing yeast cultures

Harari, Yaniv; Ram, Yoav; Kupiec, Martin

doi:10.1007/s00294-018-0823-y

Cited by 32 publications

(21 citation statements)

References 40 publications

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“…Furthermore, several events of gene duplication are present, especially abundant in scaffold VI. This phenomenon is commonly seen as a mechanism of adaptation by yeast (Hittinger and Carroll, 2007;Ames et al, 2010;Dunn et al, 2012;Gorter de Vries et al, 2017;Harari et al, 2018). For example, three repetitions of the major isomaltase IMA1 are present, displaying copy number repetitions to enhance utilization of carbon sources (Duval et al, 2010;Naumoff and Naumov, 2010;Teste et al, 2010).…”

Section: Chromosomal Organization Of the Reference B Bruxellensis Ummentioning

confidence: 99%

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

et al. 2020

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Section: Chromosomal Organization Of the Reference B Bruxellensis Ummentioning

confidence: 99%

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

et al. 2020

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“…The genetic basis of pleiotropic outcomes 177 Next, we sought to determine the genetic basis underlying the diverse pleiotropic 178 outcomes that we observed above, using two approaches. First, we used DNA staining 179 and flow cytometry (see Methods) to look for ploidy changes because this is a common 180 mode of adaptation in yeast [48][49][50][51][52]. Second, we sequenced the full genomes of the 181 evolved clones.…”

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confidence: 99%

Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast

Jerison

Desai

et al. 2019

Preprint

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Mutations that a population accumulates during evolution in one ("home") environment may cause fitness gains or losses in other conditions. Such pleiotropic fitness effects determine the evolutionary fate of the population in variable environments and can lead to ecological specialization. It is unclear how the pleiotropic outcomes of evolution are shaped by the intrinsic randomness of the evolutionary process and by the deterministic variation in selection pressures across environments. To address this question, we evolved 20 replicate populations of the yeast Saccharomyces cerevisiae in 11 laboratory environments and measured their fitness across multiple other conditions. We found that evolution in all home environments led to a diversity of patterns of pleiotropic fitness gains and losses, driven by multiple types of mutations. Approximately 60% percent of this variation are explained by clone's home environment and the most common parallel genetic changes, while about 40% are attributed to the stochastic accumulation of mutations whose pleiotropic effects are unpredictable. On average, populations specialized to their home environment, but generalists also evolved in almost all conditions. Our results suggest that the mutations accumulating in a home environment incur a variety of pleiotropic effects, from costs to benefits, with different probabilities. Therefore, whether a population evolves towards a specialist or a generalist phenotype is heavily influenced by chance.frequencies in a population adapting to one condition typically affect fitness in other 14 conditions? 15Historically, it has been assumed that pleiotropy is often antagonistic, i.e., fitness 16 benefits in one environment should often come at a fitness cost in other 17 conditions [16][17][18]. If antagonistic pleiotropy was common, it would explain why 18 ecological specialization and local adaptation are so widespread in nature. However, 19 more recent field studies have found that adaptive alleles confer fitness defects much less 20 frequently than anticipated [8,[13][14][15]19]. Although theory suggests that ecological 21 specialization and local adaptation can arise without trade-offs [20-22], it is also 22 possible that field studies provide a skewed view of the structure of pleiotropy because 23 of statistical complications and confounding factors, such as migration and unknown 24 environmental variation [23-25]. 25 Laboratory microbial and viral populations are powerful model systems where the 26 structure of pleiotropy can be probed under controlled conditions and with a degree of 27 replication seldom achievable in natural systems. Experimental populations can be 28 evolved in a laboratory environment, adaptive mutations can be identified, and the 29 fitness of evolved genotypes can be directly measured in other conditions. Several dozen 30 such studies in a variety of organisms have been carried out so far (e.g., Refs. [26-45] 31and more references in recent reviews by Elena [15] and Bono et al [14,22]). Their 32 outcomes generall...

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“…However, chromosomal mutations are typically non-neutral to fitness. Some can be beneficial and fixed by natural selection (Comai 2005; Harari et al 2018; Otto and Whitton 2000; Torres et al 2008). More frequently, they are deleterious and, therefore, eliminated either immediately or quickly enough to pass overlooked (Sheltzer and Amon 2011).…”

Section: Introductionmentioning

confidence: 99%

Gene overexpression screen for chromosome instability in yeast primarily identifies cell cycle progression genes

et al. 2018

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Loss of heterozygosity (LOH) in a vegetatively growing diploid cell signals irregularity of mitosis. Therefore, assays of LOH serve to discover pathways critical for proper replication and segregation of chromosomes. We screened for enhanced LOH in a whole-genome collection of diploid yeast strains in which a single gene was strongly overexpressed. We found 39 overexpression strains with substantially increased LOH caused either by recombination or by chromosome instability. Most of them, 32 in total, belonged to the category of “cell division”, a broadly defined biological process. Of those, only one, TOP3, coded for an enzyme that uses DNA as a substrate. The rest related to establishment and maintenance of cell polarity, chromosome segregation, and cell cycle checkpoints. Former studies, in which gene deletions were used, showed that an absence of a protein participating in the DNA processing machinery is a potent stimulator of genome instability. As our results suggest, overexpression of such proteins is not comparably damaging as the absence of them. It may mean that the harmful effect of overexpression is more likely to occur in more complex and multistage processes, such as chromosome segregation. We also report a side finding, resulting from the fact that we worked with the yeast strains bearing a 2-micron plasmid. We noted that intense transcription from such a plasmid led to an enhanced rate of an entire chromosome loss (as opposed to LOH produced by recombination). This observation may support models linking segregation of 2-micron plasmids to segregation of chromosomes.Electronic supplementary materialThe online version of this article (10.1007/s00294-018-0885-x) contains supplementary material, which is available to authorized users.

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Frequent ploidy changes in growing yeast cultures

Cited by 32 publications

References 40 publications

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast

Gene overexpression screen for chromosome instability in yeast primarily identifies cell cycle progression genes

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