Prions are a common mechanism for phenotypic inheritance in wild yeasts

Abstract

The self-templating conformations of yeast prion proteins act as epigenetic elements of inheritance. Yeast prions might provide a mechanism for generating heritable phenotypic diversity that promotes survival in fluctuating environments and the evolution of new traits. However, this hypothesis is highly controversial. Prions that create new traits have not been found in wild strains, leading to the perception that they are rare 'diseases' of laboratory cultivation. Here we biochemically test approximately 700 wild strains of Saccharomyces for [PSI(+)] or [MOT3(+)], and find these prions in many. They conferred diverse phenotypes that were frequently beneficial under selective conditions. Simple meiotic re-assortment of the variation harboured within a strain readily fixed one such trait, making it robust and prion-independent. Finally, we genetically screened for unknown prion elements. Fully one-third of wild strains harboured them. These, too, created diverse, often beneficial phenotypes. Thus, prions broadly govern heritable traits in nature, in a manner that could profoundly expand adaptive opportunities.

Figure 1

Identification and verification of prions in wild yeast. a, A representative SDD-AGE blot of wild yeast isolates probed with antibodies against Sup35 and Rnq1. Amyloid polymers produce characteristic smears. SDD-AGE does not reliably detect monomeric proteins. b, Transient inactivation of Hsp104 by GdHCl or expression of a dominant negative mutant of Hsp104 eliminates these amyloids, indicating that they are [PSI⁺] and [RNQ⁺] prions.

Figure 2

Prion-contingent phenotypes of [PSI+] isolates. a, Wild [PSI⁺] strains show diverse phenotypes that are eliminated by transient Hsp104 inhibition. Growth curves for wild strains and cured derivatives in the indicated selective condition are in closed blue circles and open red circles, respectively. Growth in YPD is presented for each wild strain (closed grey circles) and its cured derivative (open grey circles) as a control. OD600, optical density measured at 600 nm. b, Phenotypes of the wild [PSI+] strains were also eliminated by expression of Sup35ΔPrD. Growth curves for wild strains expressing Sup35 or Sup35ΔPrD in the indicated selective condition are in closed blue circles and open red circles, respectively. Growth in YPD for the indicated wild strain expressing Sup35 (closed grey circles) or Sup35ΔPrD (open grey circles) is presented as a control. Error bars are present on all points and represent the standard deviation from four independent biological replicates.

Figure 3

Genetic assimilation of the [PSI⁺]-dependent adhesive phenotype in meiotic progeny of UCD978. a, [PSI⁺] allows the wine yeast UCD#978 to adhere to agar surfaces. Adhesion is eliminated by GdHCl or by b, Expression of a non-aggregating version of Sup35, Sup35ΔPrD. c, Meiotic progeny of strain UCD#978 show a diversity of phenotypes. In some spores the adhesive phenotype was assimilated and remained even after the [PSI⁺] prion was cured. In others the adhesive phenotype retained [PSI⁺] dependence. Finally, some lost the phenotype altogether, irrespective of [PSI⁺] status.

Figure 4

Prions of the cell wall-remodelling transcription factor, Mot3, have diverse phenotypic consequences in wild strains. a, Strain Y-35 is resistant to the cell wall targeting drug, calcofluor white, but resistance is strongly reduced by passage on GdHCl. Probing for Mot3’s endogenous hexa-histidine motif reveals that Mot3 amyloids are retained in the uncured, but not the cured isolates. Apparent monomeric signal results from cross-reactivity to other yeast proteins. b, The [MOT3⁺] strains NCYC#3311 and Y-1537 (each shown in filled blue circles) are resistant to acidic growth conditions and fluconazole, respectively. Each phenotype is reversed by prion curing with GdHCl passage (open red circles). c, These phenotypes are also reversed by expression of a non-aggregating version of Mot3, Mot3ΔPrD (open red circles). Expression of Mot3 itself (closed blue circles) did not affect the phenotype of either strain. Error bars represent the standard deviation of four independent biological replicates.

Figure 5

The curable Hsp104-dependent epigenetic elements in wild yeast can be cytoplasmically transferred. a, Growth of wild strains WE372, YJM428, and their cured derivatives in selective conditions. Original isolates of each strain are shown in grey bars and their cured derivatives (indicated by black arrows) are shown in open bars. Error bars are one standard deviation from six biological replicates. b, Schematic for cytoduction experiments and control to ensure that phenotypes are due to prions, rather than transfer of mitochondrial DNA. c, Growth measurements of the laboratory recipient (blue bars), cytoductants (grey bars; red arrows denote cytoplasmic transfer of phenotypes), and cured derivatives of those cytoductants (open bars; black arrows denote curability of phenotypes). Error bars are the standard deviation of growth measurements from 12 cytoductants, the 12 cured derivatives of those cytoductants, or 6 biological replicates of the recipient strain. d, Cytoductants that received cytoplasm from cured derivatives of the original wild isolates (hashed bars) did not show an equivalent change in phenotype. Error bars represent the standard deviation of growth measurements from 12 cytoductants or six biological replicates of the recipient strain.