Pioneer cells established by the [<i>SWI</i>⁺] prion can promote dispersal and out-crossing in yeast

<div><p>To thrive in an ever-changing environment, microbes must widely distribute their progeny to colonize new territory. Simultaneously, they must evolve and adapt to the stresses of unpredictable surroundings. In both of these regards, diversity is key—if an entire population moved together or responded to the environment in the same way, it could easily go extinct. Here, we show that the epigenetic prion switch [<i>SWI</i>⁺] establishes a specialized subpopulation with a “pioneer” phenotypic program in <i>Saccharomyces cerevisiae</i>. Cells in the pioneer state readily disperse in water, enabling them to migrate and colonize new territory. Pioneers are also more likely to find and mate with genetically diverse partners, as inhibited mating-type switching causes mother cells to shun their own daughters. In the nonprion [<i>swi</i>^<i>−</i>] state, cells instead have a “settler” phenotype, forming protective flocs and tending to remain in their current position. Settler cells are better able to withstand harsh conditions like drought and alkaline pH. We propose that these laboratory observations reveal a strategy employed in the wild to rapidly diversify and grant distinct, useful roles to cellular subpopulations that benefit the population as a whole.</p></div

Flow cytometry gating strategies

The gating strategy for each flow cytometry experiment is described, with accompanying pictures of gates

Data graphed in Newby and Lindquist 2017

The data used to prepare graphs is given in a Microsoft Excel file. Each worksheet name indicates the figure that was generated from the data given

[<i>SWI</i>⁺] cells have lower fitness and do not survive dry conditions.

<p>(A) The survival of [<i>SWI</i>⁺] (red) and [<i>swi</i>^<i>−</i>] (blue) cells from overnight cultures (no stress), 6-day–starved cultures (starvation), and antifungal-treated overnight cultures (amphotericin B and caspofungin) were measured using a viability stain and flow cytometry. Error bars indicate standard deviation (<i>n</i> = 3). All numerical data in this figure and the flow cytometry gating strategy are available from the Dryad Digital Repository: <a href="https://doi.org/10.5061/dryad.d5r16" target="_blank">http://dx.doi.org/10.5061/dryad.d5r16</a>. (B) Growth comparison of [<i>swi</i>^<i>−</i>] cells and [<i>SWI</i>⁺] cells in media buffered at pH 7.5. Cell density was measured by absorbance every 15 minutes. (C) Survival of [<i>SWI</i>⁺] and [<i>swi</i>^<i>−</i>] cultures after removal of liquid media followed by drying under blowing air for 24 hours. The survival of [<i>SWI</i>⁺] was below the detection limit using viability stain and flow cytometry (1 in 10,000 cells). Error bars indicate standard deviation (<i>n</i> = 3). (D) Recovery of dried [<i>SWI</i>⁺] and [<i>swi</i>^<i>−</i>] strains in liquid culture in microtiter plates. After rehydration of dried cells into the original volume of the liquid culture, a 25-fold dilution into fresh media was made in microtiter wells. Growth after four days is depicted.</p

The [<i>SWI</i>⁺] prion enhances the migration of cells with the flow of water.

<p>(A) A diagram of the experimental procedures used to test the migration of cells on solid media. Pregrown spots of yeast colonies experience “rainfall” as drops of water are pipetted over them. The plates are tilted to allow the water to flow across the surface. After drying and incubating for yeast growth, colonies established by the migrated cells appear. (B) Photograph showing the migration of [<i>swi</i>^<i>−</i>] and [<i>SWI</i>⁺] cells on an agar plate. (C) Quantification of total cell number after the migration experiment. Error bars indicate standard deviation (<i>n</i> = 3). Numerical data are available from the Dryad Digital Repository: <a href="https://doi.org/10.5061/dryad.d5r16" target="_blank">http://dx.doi.org/10.5061/dryad.d5r16</a>. (D) Left: Photograph showing the migration of cells on an agar plate after [<i>SWI</i>⁺] and [<i>swi</i>^<i>−</i>] cells were mixed in the indicated proportions. Arrows indicate large colonies where small flocs of [<i>swi</i>^<i>−</i>] cells have migrated. Center: The same image collected in a green fluorescence channel. Due to the yTRAP sensor [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003476#pbio.2003476.ref015" target="_blank">15</a>] in both strains, [<i>swi</i>^<i>−</i>] colonies are brightly fluorescent. Right: Migration experiment from panel B photographed in the green fluorescence channel for comparison. yTRAP, yeast transcriptional reporting of aggregating proteins.</p

The [<i>SWI</i>⁺] prion encourages diverse mating partners.

<p>(A) A diagram showing the mating tendencies of [<i>SWI</i>⁺] and [<i>swi</i>^<i>−</i>] haploids (budding yellow cell). Left: A [<i>swi</i>^<i>−</i>] cell will readily switch its mating type after dividing and mate with its own daughter. The resulting diploid cannot out-cross with diverse mating partners (orange cell). Right: In the [<i>SWI</i>⁺] pioneering state, mating-type switching is inhibited, and thus mother cells cannot mate with their own daughters. This increases the likelihood that they will mate with genetically diverse partners. Note that after normal mating-type switching, an additional generation may occur before mating, after which the four haploids involved can mate in pairs (not depicted). (B) Relative out-crossing efficiencies of [<i>swi</i>^<i>−</i>] cells (blue) and [<i>SWI</i>⁺] cells (red). Elimination of the prion from the [<i>SWI</i>⁺] strain (“cured”) returns its out-cross ratio to the low state. The ratio was calculated by normalizing to the mating efficiency of <i>ho</i>^<i>−</i> control cells (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003476#pbio.2003476.s002" target="_blank">S2A Fig</a>). Error bars indicate standard deviation (<i>n</i> = 3). Numerical data and the flow cytometry gating strategy are available from the Dryad Digital Repository: <a href="https://doi.org/10.5061/dryad.d5r16" target="_blank">http://dx.doi.org/10.5061/dryad.d5r16</a>.</p