Adaptive Potential of Epigenetic Switching During Adaptation to Fluctuating Environments

Abstract

Epigenetic regulation of gene expression allows for the emergence of distinct phenotypic states within the clonal population. Due to the instability of epigenetic inheritance, these phenotypes can intergenerationally switch between states in a stochastic manner. Theoretical studies of evolutionary dynamics predict that the phenotypic heterogeneity enabled by this rapid epigenetic switching between gene expression states would be favored under fluctuating environmental conditions, whereas genetic mutations, as a form of stable inheritance system, would be favored under a stable environment. To test this prediction, we engineered switcher and non-switcher yeast strains, in which the uracil biosynthesis gene URA3 is either continually expressed or switched on and off at two different rates (slow and fast switchers). Competitions between clones with an epigenetically controlled URA3 and clones without switching ability (SIR3 knockout) show that the switchers are favored in fluctuating environments. This occurs in conditions where the environments fluctuate at similar rates to the rate of switching. However, in stable environments, but also in environments with fluctuation frequency higher than the rate of switching, we observed that genetic changes dominated. Remarkably, epigenetic clones with a high, but not with a low, rate of switching can coexist with non-switchers even in a constant environment. Our study offers an experimental proof of concept that helps defining conditions of environmental fluctuation under which epigenetic switching provides an advantage.

Keywords: adaptation; epigenetic switching; fluctuating environments; mutations.

Fig. 1.

Experimental setup. Scheme showing experimental evolution setup used in the study. Yeast strains with epigenetic silencing (labelled with RFP) and a SIR3 knockout strain (labelled with YFP) were preselected in media without uracil (i.e., selection for active URA3 gene) and mixed in 1:100 proportions, respectively. Subsequently, the mixed RFP/YFP yeast cultures were exposed to environments that fluctuated with different periodicity. Each box represents a 24-h period after which populations were sampled and relative ratio of strains were determined. The color of the boxes represents the selection regime whereby gray boxes indicate selection for the inactive form of URA3 and white-colored boxes indicate selection for the active form of URA3.

Fig. 2.

Epigenetic switchers dominate during adaptation to fluctuating environments. (A) Survival through the course of selection in the three fluctuating environments with distinct periodicities, determined using FACS methodology. Each line represents the number of cells in each replicate population (24 replicate populations for each environmental condition). Colored areas indicate the selection regime, gray corresponds to selection for inactive URA3 and white for selection for the active form of the gene. (B) Dynamics of RFP/YFP ratios (with high rate of epigenetic switching) in fluctuating environments. The logarithm of RFP/YFP ratios for each of the replicate populations is shown, determined using FACS methodology. The color of the line for each population corresponds to the color of the lines in the survival graphs. Colored areas indicate the selection regime, gray corresponds to selection for inactive URA3 and white to selection for the active form of the gene. Positive values indicate dominance of the RFP strain, and negative values indicate dominance of the YFP strain.

Fig. 3.

Epigenetic switchers coexist with non-switchers in stable environments. (A) Survival through the course of selection for two constant environments with distinct selection regimes here marked with the same colors as in the fluctuating environments (gray indicates selection for an inactive URA3 gene and white for an active form of the gene), determined using FACS methodology. Each line represents the number of cells in each replicate population over time (24 replicate populations for each environmental condition). (B) Dynamics of RFP/YFP ratios in the two constant environments. The logarithm of RFP/YFP ratios for each of the replicate populations is shown, determined using FACS methodology. The color of the line for each population corresponds to the color of the lines in survival graphs. Colored areas indicate the selection regime as in panel A.

Fig. 4.

Populations selected in fluctuating environments show a higher frequency of the epigenetic switcher strain than those grown in stable environments. We compared the frequency of the fast epigenetic switcher strain at the final time point across all selection regimes. Points represent frequencies for each replicate population. For each selection regime the mean value across population replicates is plotted. The mean values between the selection regimes were compared using Dunn’s nonparametric test with Bonferroni correction for multiple testing (n = 10).

Fig. 5.

The advantage of epigenetic switching is dependent on the period of environmental fluctuation. (A) Points represent frequencies of clones that were able to grow on both the plates containing 5-FOA (selecting for OFF state of URA3 gene) and the plates lacking uracil (selecting for the ON state of URA3 gene) within each replicate population at the end of the experiment. Bars represent the mean and standard deviation. The mean values between the selection regimes were compared using Dunn’s nonparametric test with Bonferroni correction for multiple testing (n = 3). (B) Points represent frequencies of clones whose 5-FOA resistance was not abrogated upon the addition of the inhibitor of epigenetic silencing, nicotinamide, within each replicate population. Bars represent the mean and standard deviation. The mean values between the selection regimes were compared using Dunn’s nonparametric test with Bonferroni correction for multiple testing (n = 3).

Fig. 6.

The dynamics of epigenetic switchers depend on the rate of epigenetic switching. (A) Survival through the course of selection for a strain with a low rate of epigenetic switching in the three fluctuating environments with distinct periodicities, determined using FACS methodology. Each line represents number of cells in each replicate population (24 replicate populations for each environmental condition). Colored areas indicate the selection regime, gray corresponds to selection for inactive URA3 and white for selection for the active form of the gene. (B) Dynamics of RFP/YFP ratios (with a low rate of epigenetic switching) in the fluctuating environments. The logarithm of RFP/YFP ratios for each of the replicate populations is shown, determined using FACS methodology. The color of the line for each population corresponds to the color of the lines in survival graphs. Colored areas indicate the selection regime as in panel A. Positive values indicate dominance of RFP strain, and negative dominance of YFP strain.

Fig. 7.

Schematic representation of the results. (A) In fluctuating environments where the conditions select for distinct gene expression state (blue and red background), mechanisms that enable stochastic switching between two phenotypes (red and blue cells) will be favored over a stable phenotypic determinant (yellow cells). Due to the slow rate of change, genetic mutations (brown cells) have little impact in a changing environment. (B) In a stable environment, epigenetic switching might provide an initial advantage to the survival of the population. However, once genetic mutations appear they would sweep to fixation.