Heat shock drives genomic instability and phenotypic variations in yeast

Abstract

High temperature causes ubiquitous environmental stress to microorganisms, but studies have not fully explained whether and to what extent heat shock would affect genome stability. Hence, this study explored heat-shock-induced genomic alterations in the yeast Saccharomyces cerevisiae. Using genetic screening systems and customized single nucleotide polymorphism (SNP) microarrays, we found that heat shock (52 °C) for several minutes could heighten mitotic recombination by at least one order of magnitude. More than half of heat-shock-induced mitotic recombinations were likely to be initiated by DNA breaks in the S/G₂ phase of the cell cycle. Chromosomal aberration, mainly trisomy, was elevated hundreds of times in heat-shock-treated cells than in untreated cells. Distinct chromosomal instability patterns were also observed between heat-treated and carbendazim-treated yeast cells. Finally, we demonstrated that heat shock stimulates fast phenotypic evolutions (such as tolerance to ethanol, vanillin, fluconazole, and tunicamycin) in the yeast population. This study not only provided novel insights into the effect of temperature fluctuations on genomic integrity but also developed a simple protocol to generate an aneuploidy mutant of yeast.

Keywords: Aneuploidy; Heat shock; Mitotic recombination; Phenotypic evolution; Yeast.

Fig. 1

Heat shock stimulates mitotic recombination in the yeast strain JSC25-1. a A reciprocal crossover event on the right arm of chromosome IV would produce white/red-sectored JSC25-1 colonies. Alternatively, break-induced replication (nonreciprocal crossover) would produce white/pink- or red/pink-sectored colonies. b Cell viability of the JSC25-1 yeast strain after heat shock exposure (52 °C) for 2–4 min. c Reciprocal crossover frequency determined by calculating the red/white-sectored colonies formed on YPD plates after heat shock. “*” indicates significant difference at the level of 0.01 using t-test

Fig. 2

Analysis of crossover events by chr IV-specific SNP microarray. The Y-axis values show the normalized hybridization ratio (HR) of genomic DNA to oligonucleotides that are specific to W303-1A- and YJM789-derived SNPs. The X-axis values indicate the SGD coordinates of the SNPs. The hybridization ratio values of about 0.2, 1, 1.5 represent 0, 1, and 2 homolog copies, respectively. The red and blue lines/points indicate the HR of W303-1A- and YJM789-derived SNPs, respectively. The analysis results of the white sector and the red sector are shown in a and b at low resolution; the high-resolution results are shown in c and d. e The gene conversion tract pattern associated with this crossover event

Fig. 3

Whole-genome mapping of heat-shock-induced genomic alterations in the 21 JSC25-1-derived isolates treated with heat shock. a LOH events detected on chr X in the JSC25-1-derived isolate JP14. b Patterns of genetic events. The red and blue lines represent W303-1A- and YJM789-derived homologs, respectively. The gray lines indicate heterozygous regions. Classes a1–a4 represent terminal LOH events; b1, b2 and c1 represent gene conversion events; and d1 represents deletion event. c The genetic event distribution across the 16 chromosomes. The yellow vertical lines represent SNP sites

Fig. 4

Aneuploidy events observed in the JSC25-1-derived isolates. The SNP results in a–c indicate trisomy, monosomy, and UPD event, respectively. d Heat-shock-induced aneuploidy events in the 21 JSC25-1-derived isolates. Red, orange, yellow, light yellow, blue, and dark blue represent pentasomy, tetrasomy, trisomy, uniparental disomy, normal, and monosomy, respectively

Fig. 5

Chromosomal instability resulting from carbendazim treatment in JSC25-1. Genomic alterations were detected in 40 carbendazim-treated isolates (MT1–MT40) by the chr IV–specific SNP microarray. a An example of a carbendazim-induced terminal LOH event on the right arm of chr IV. b A terminal deletion event on the right arm of chr III. c A terminal LOH duplication event on the left arm of chr XIV. The genetic events in b and c were observed in the same isolate. d Aneuploidy events resulted from carbendazim treatment. Orange, yellow, light yellow, blue, and dark blue represent tetrasomy, trisomy, uniparental disomy, normal, and monosomy, respectively

Fig. 6

Heat shock drives fast phenotypic variations in yeast population. Experiments were performed three times, and the means are shown here. Error bars represent the standard deviation. a The frequency of resistant JSC25-1 isolates appeared on the solid YPD medium containing 120 g/L ethanol, 0.3 mg/L fluconazole, 1.2 g/L vanillin, and 4 mg/L tunicamycin. In this experiment, about 1 × 10^–4 viable cells were plated on each plate. b Comparison of biomass formation (OD₆₀₀) in yeast isolates in liquid YPD medium containing 70 g/L ethanol (E1–E5), 0.15 mg/L fluconazole (F1–F5), 0.8 g/L vanillin (V1–V5), and 1.5 mg/L tunicamycin (T1–T5). The OD₆₀₀ of each sample was determined at the 12 h time point. The JSC25-1 parental strain is indicated by “p”