Chromosomal duplication is a transient evolutionary solution to stress

Abstract

Aneuploidy, an abnormal number of chromosomes, is a widespread phenomenon found in unicellulars such as yeast, as well as in plants and in mammalians, especially in cancer. Aneuploidy is a genome-scale aberration that imposes a severe burden on the cell, yet under stressful conditions specific aneuploidies confer a selective advantage. This dual nature of aneuploidy raises the question of whether it can serve as a stable and sustainable evolutionary adaptation. To clarify this, we conducted a set of laboratory evolution experiments in yeast and followed the long-term dynamics of aneuploidy under diverse conditions. Here we show that chromosomal duplications are first acquired as a crude solution to stress, yet only as transient solutions that are eliminated and replaced by more efficient solutions obtained at the individual gene level. These transient dynamics of aneuploidy were repeatedly observed in our laboratory evolution experiments; chromosomal duplications gained under stress were eliminated not only when the stress was relieved, but even if it persisted. Furthermore, when stress was applied gradually rather than abruptly, alternative solutions appear to have emerged, but not aneuploidy. Our findings indicate that chromosomal duplication is a first evolutionary line of defense, that retains survivability under strong and abrupt selective pressures, yet it merely serves as a "quick fix," whereas more refined and sustainable solutions take over. Thus, in the perspective of genome evolution trajectory, aneuploidy is a useful yet short-lived intermediate that facilitates further adaptation.

Fig. 1.

Laboratory evolution (Lab-evolution) tree describing the experimental outline. Each evolution experiment starts with an ancestor strain (gray box) that was subjected to certain growth conditions: high temperature, 39 °C (red); permissive temperature, 30 °C (blue); gradually increasing temperature, from 30 °C to 39 °C (gradient line); and high pH 8.6 (green). Parallel lines splitting from the same branch represent independent repetitions and their length is in scale with the number of generations under the specified condition. Evo39 strain was taken after 450 generations on high temperature (39 °C) as an ancestor for another two evolutionary branches (Refined 1–4 and Relaxed 1–4). Microarray icons represent points during the evolution tree in which such measurement was performed.

Fig. 2.

Aneuploidy appears and subsequently was eliminated during evolutionary adaptation to heat. Four independent repetitions (H1–4) that evolved for 450 generations in rich medium and heat (39 °C) show chromosomal duplications (black lines). Notably, duplication of chromosome III occurred in all four repetitions. H2 and H4, which carry no large-scale duplication other than chromosome III trisomy, were further evolved under the same conditions and after 1,700 generations (magenta lines) and 2,350 generations (green line), the trisomy was eliminated. All lines represent log₂ intensity ratios of mRNA abundance calculated by a sliding window of heat-evolved strain over a diploid wild type, aligned according to chromosomal order where blue vertical lines differentiate between chromosomes.

Fig. 3.

An extra copy of chromosome III is beneficial under heat, yet it is maladaptive under other conditions. (A) Heat-shock tolerance rates are proportional to the copy number of chromosome III. Heat-shock survival fold change of chromosome III aneuploidic strains compared with a diploid wild type is shown (dashed line). (B) The extra copy of chromosome III is the predominant genetic trait responsible for the increased heat tolerance. Heat-shock survival fold change of spores from WTtrisomeIII and evo39, compared with a haploid wild type (dashed line), presented separately for euploid spores and for chromosome III disomic spores (P value < 8 × 10⁻⁵; for spore karyotype, see Fig. S7). (C) The growth advantage conferred by chromosome III trisomy under heat (red line) cannot be attributed to a general stress tolerance. Colored lines represent OD ratios of WTtrisomeIII over a diploid wild type during continuous growth under various stresses (Materials and Methods). (D) The cost of chromosome III trisomy at permissive temperature (30 °C) is increased on minimal medium compared with rich medium. Growth curve measurements of WTtrisomeIII (red) and of a diploid wild type (green) are shown in OD values over time during continuous growth at 30 °C (Upper), in rich medium (Left) and in minimal medium (Right). (Lower) Growth rate analyses, derived from the OD values, and the differences in minimal doubling time between WTtrisomeIII and WT. Data are presented as mean and SEM.

Fig. 4.

The aneuploidy-based adaptation was evolutionarily eliminated and replaced by more economical solutions based on refined gene expression adaptations. (A) Descendants of chromosome III trisomic ancestors that were further evolved under heat and lost the trisomy (Refined 1–4) show improved growth under heat, yet with less cost compared with their trisomic ancestors. Each subgraph shows the OD ratios of a refined descendant over its trisomic ancestor measured during continuous growth at 30 °C (Upper) and at 39 °C (Lower). (B) Despite elimination of the trisomy in Refined 1–4, a group of genes from chromosome III retained high expression levels. Dots represent log₂ ratios of mRNA abundance of chromosome III genes over a diploid wild type. Genes that retain high expression (in at least three of the four refined evolutions; for details see SI Text) are marked in red, and from the majority of genes that went back to wild-type–like expression (gray dots) a control group was selected and marked in black (used in C). These retained genes were also up-regulated in H2 and H4, which also eliminated the trisomy (χ² P values 4 × 10⁻⁵ and 3 × 10⁻²). (C) The group of genes that retain high expression levels, after the elimination of the trisomy, confers increased heat tolerance when introduced into wild type. Each of the highly expressed genes (red) and the negative control genes (black) was inserted into the diploid wild type, on a centromeric plasmid, and heat-shock tolerance was compared with the heat tolerance of WTtrisomeIII (t test P value < 5 × 10⁻⁷; Materials and Methods). (D) The refined solution replacing the trisomy is characterized by changes in expression levels of most HSP genes. Log₂ expression ratios over wild type are shown for all HSPs, for trisomic evo39 (blue) and its descendants that eliminated the trisomy (red). Data are presented as mean and SEM.

Fig. 5.

Evolution on high pH selects for transient duplication of chromosome V, which is later eliminated. (A) Haploid wild type that evolved under high pH (27) acquired chromosome V disomy (Top subgraph). We identified two spores obtained from crossing the disomic evolved strain with a haploid wild type. These spores carry the same mutation subset (Table S2) but differ in the copy number of chromosome V (Middle and Bottom subgraphs). Black lines represent log₂ intensity ratios of mRNA abundance calculated by a sliding window over a haploid wild type, aligned according to chromosomal order where blue vertical lines differentiate between chromosomes. (B) An extra copy of chromosome V confers high-pH (8.6) tolerance but causes impaired growth on normal pH (6.7). Growth curves of disomic spore (red) and euploid spore (green) under high pH (Upper) and normal pH (Lower). (C) Chromosome V disomy, gained by EvoHigh-pH after 150 generations at high pH (black lines), is eliminated during further evolution under the same high pH in which it was originally gained. Four independent descendants of EvoHigh-pH (pH Refined 1–4) continued to evolve for 600 generations at high pH (8.6). All evolved populations show elimination of the disomy (magenta lines) with two populations showing complete elimination (Left two) and the other two populations showing the majority of the population's cells eliminate the disomy (Right two). All lines represent log₂ intensity ratios of mRNA abundance calculated by a sliding window of the high pH evolved strain over a haploid wild type, aligned according to chromosomal order where blue vertical lines differentiate between chromosomes.