The Spontaneous Appearance Rate of the Yeast Prion [PSI+] and Its Implications for the Evolution of the Evolvability Properties of the [PSI+] System

Abstract

Epigenetically inherited aggregates of the yeast prion [PSI1] cause genomewide readthrough translation that sometimes increases evolvability in certain harsh environments. The effects of natural selection on modifiers of [PSI1] appearance have been the subject of much debate. It seems likely that [PSI1] would be at least mildly deleterious in most environments, but this may be counteracted by its evolvability properties on rare occasions. Indirect selection on modifiers of [PSI1] is predicted to depend primarily on the spontaneous [PSI1] appearance rate, but this critical parameter has not previously been adequately measured. Here we measure this epimutation rate accurately and precisely as 5.8 3 10 À7 per generation, using a fluctuation test. We also determine that genetic ''mimics'' of [PSI1] account for up to 80% of all phenotypes involving general nonsense suppression. Using previously developed mathematical models, we can now infer that even in the absence of opportunities for adaptation, modifiers of [PSI1] are only weakly deleterious relative to genetic drift. If we assume that the spontaneous [PSI1] appearance rate is at its evolutionary optimum, then opportunities for adaptation are inferred to be rare, such that the [PSI1] system is favored only very weakly overall. But when we account for the observed increase in the [PSI1] appearance rate in response to stress, we infer much higher overall selection in favor of [PSI1] modifiers, suggesting that [PSI1]-forming ability may be a consequence of selection for evolvability.

The ribosome-associated complex antagonizes prion formation in yeast

“…In wildtype cells, the rate of prion formation was determined to be 2.68 £ 10 ¡7 with a confidence interval of (1.33-5.40) £ 10 ¡7 , in agreement with previous findings. 39 However, cells lacking RAC function exhibit a prion formation rate nearly 7-fold greater than in wildtype cells (1.83 £ 10 ¡6 with a confidence interval of (1.24-2.71) £ 10 ¡6 ). Thus, 39,41 with error bars representing the 95% confidence intervals (nD10).…”

“…39 However, cells lacking RAC function exhibit a prion formation rate nearly 7-fold greater than in wildtype cells (1.83 £ 10 ¡6 with a confidence interval of (1.24-2.71) £ 10 ¡6 ). Thus, 39,41 with error bars representing the 95% confidence intervals (nD10). (C) Relative abundance of Ssa1/2 (Ssa), Ssb1/2 (Ssb), Hsp104, Sis1 and Ydj1 in wildtype and Dzuo1 strains expressing each chaperone as a carboxyl-terminal GFP fusion from its endogenous promoter and natural chromosomal location.…”

“…Because spontaneous prion formation in the absence of Sup35NM over-expression is a low frequency event, 39 large numbers of cells must be plated to identify [PSI C ] cells and thus spontaneous mutations affecting the ade1-14 reporter system could potentially confound the results. We therefore employed 2 nonsense suppression reporters to determine whether functional RAC is required for suppression of spontaneous prion formation: the ade1-14 allele and the ura3-14 allele.…”

“…We therefore employed 2 nonsense suppression reporters to determine whether functional RAC is required for suppression of spontaneous prion formation: the ade1-14 allele and the ura3-14 allele. 40 We used Luria-Delbruck fluctuation analysis to estimate [PSI C ] formation rates with 95% confidence intervals 39,41 by measuring conversion to Ade C Ura C in single colonies grown from individual [psi ¡ ] cells (Fig. 1B).…”

The sensitive [SWI+] prion

“…The uninduced rate of [PSI + ] formation, that is, the rate uninfluenced by protein overexpression or environmental stresses, was recently reported to be 5.7 x 10 -7 /cell/generation. 25 In contrast, some, if not all, of the N-rich prions discussed above form at much higher rates ( Table 2 11 While they note that they tried the experiment several times before succeeding, the ability to detect spontaneous [SWI + ] formation from a relatively small yeast cell population strongly suggests that [SWI + ] appears significantly more often than [PSI + ], which would only be expected to appear at a rate of 5 out of 10,000,000 ©2 0 1 1 L a n d e s B i o s c i e n c e .…”