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Yeasts collectively extend the limits of habitable temperatures by secreting glutathione

Nature Microbiology volume 5, pages 943–954 (2020)Cite this article

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Abstract

The conventional view is that high temperatures cause microorganisms to replicate slowly or die. In this view, microorganisms autonomously combat heat-induced damages. However, microorganisms co-exist with each other, which raises the underexplored and timely question of whether microorganisms can cooperatively combat heat-induced damages at high temperatures. Here, we use the budding yeast Saccharomyces cerevisiae to show that cells can help each other and their future generations to survive and replicate at high temperatures. As a consequence, even at the same temperature, a yeast population can exponentially grow, never grow or grow after unpredictable durations (hours to days) of stasis, depending on its population density. Through the same mechanism, yeasts collectively delay and can eventually stop their approach to extinction, with higher population densities stopping faster. These features arise from yeasts secreting and extracellularly accumulating glutathione—a ubiquitous heat-damage-preventing antioxidant. We show that the secretion of glutathione, which eliminates harmful extracellular chemicals, is both necessary and sufficient for yeasts to collectively survive at high temperatures. A mathematical model, which is generally applicable to any cells that cooperatively replicate by secreting molecules, recapitulates all of these features. Our study demonstrates how organisms can cooperatively define and extend the boundaries of life-permitting temperatures.

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Fig. 1: Conventional cell-autonomous view of temperature-dependent cell replication.
Fig. 2: Population density determines the replicability of cells and habitability of each temperature.
Fig. 3: Cells collectively combat death to avoid extinction high temperatures.
Fig. 4: Cells secrete and extracellularly accumulate glutathione to help each other and future generations of cells to replicate at high temperatures.
Fig. 5: Mathematical model with one free parameter recapitulates all of the main experimental data.
Fig. 6: Budding yeast exports glutathione of which the extracellular, but not intracellular, role as an antioxidant enables yeast to survive high temperatures.

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Data availability

All data supporting the findings of this study are available within the paper and its Supplementary Information. RNA-seq data are available at NCBI GEO (GSE137151). Source data for Figs. 2–4 and 6 are provided with the paper. The data that support the findings of this study are available from the corresponding author on reasonable request.

Code availability

All scripts used for simulations in this research are publicly available (GitHub diederiklt/YeastHighTemperatures).

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Acknowledgements

We thank S. Itzkovitz and A. Raj for comments on our manuscript; the members of the Youk laboratory for helpful discussions; and M. Mohebbi for help with initial experiments. H.Y. was supported by the European Research Council (ERC) Starting Grant (MultiCellSysBio, no. 677972), the Netherlands Organisation for Scientific Research (NWO) Vidi award (no. 680-47-544), the CIFAR Azrieli Global Scholars Program and the EMBO Young Investigator Award.

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Authors and Affiliations

  1. Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands

    Diederik S. Laman Trip & Hyun Youk

  2. Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands

    Diederik S. Laman Trip & Hyun Youk

  3. CIFAR, CIFAR Azrieli Global Scholars Program, Toronto, Ontario, Canada

    Hyun Youk

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Contributions

H.Y. initiated this research and performed the initial growth experiments. D.S.L.T. subsequently designed additional experiments with guidance from H.Y. D.S.L.T. performed all of the experiments, developed the mathematical model and analysed the data with advice from H.Y. D.S.L.T. and H.Y. discussed and checked all of the data and wrote the manuscript.

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Correspondence to Hyun Youk.

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Extended data

Extended Data Fig. 1 A few cells stochastically and transiently replicate within populations that are in either no-growth or random-growth phase (Related to Fig. 2a–d).

a, The wild-type strain lacks a functional ADE2 gene for synthesizing adenine. Since we incubated yeasts in the minimal media with all the essential nutrients - including adenine - the wild-type cells were still capable of growing. But having a defective ade2 gene turns yeasts red if they have not divided for some time because they have accumulated red pigments - these are by-products of the not-fully-repressed and defective adenine-biosynthesis. The cells can only dilute away the red pigments through cell divisions. The histogram shows percentages of red cells (non-replicators) and ‘white cells’ (non-red, replicators) in a population, determined by a flow cytometer’s red-fluorescence detector that quantified redness of individual cells. b, Percentage of white and red cells over time measured with the flow cytometer for a population of wild-type yeasts. Time shows hours of incubation in 38.4 OC. These histograms show example time courses for a population that grew at a high temperature. c, Numbers of white and red cells in a population per ml, at various times for three different growth regimes indicated by the phase diagram (Fig. 2d). Random-growth phase shows two replicate populations - one growing (second row) and one not growing (third row).

Extended Data Fig. 2 The number of survivors decreasing over time as a heavy-tailed function is not due to heat-tolerant mutants or persistor-like cells existing within a population (Related to Fig. 3a, b).

a-b, The number of survivors per ml over time for populations of wild-type cells kept in the no-growth phase at 42.0 OC (Supplementary Fig. 6). The brown dashed lines represent an exponentially decaying function fitted to the data points that lie between 10 h and 50 h. The blue dashed curve is a power-law function fitted to the same data points. a, The number of surviving wild-type cells. Triangles are overestimates (i.e., the aliquots taken from the liquid culture at 42 OC did not yield any colonies on agar at 30 OC, so there could not have been more survivors in the liquid culture than values represented by the triangles). We observed eight colonies formed at the last time point (~220 h - the last circle). b, We took one of these eight colonies - progenies of the survivors from the last time point in a - and used the cells from this colony to repeat the experiment. The number of survivors in this new experiment also decreased over time as a heavy-tailed function. This result eliminates the possibility that the survivors of the high temperature (42 OC) in the first experiment a are either heat-tolerant mutants or persistor-like cells that behave similarly to persistors of antibiotic treatments. To see this, suppose that the survivors at the last time point in a were heat-tolerant mutants or persistor-like cells. Then the starting population in b must be a pure population of these heat-tolerant mutants or persistor-like cells, that would have died at a slower rate than all the other cells of the wild-type population that started in a. It then follows that the number of survivors per ml in b should decrease as a single, slowly decaying exponential function rather than decreasing over time as a heavy-tailed function. Thus, by contradiction, the survivors at high temperatures are not heat-tolerant mutants or persistor-like cells.

Extended Data Fig. 3 Mathematical model reproduces the sustained population of few replicating cells in random-growth and no-growth phases (Related to Extended Data Fig. 1).

a, The number of alive (yellow) and dead cells (red) over time. The same, fixed set of parameters was used as in Fig. 5. Depending on the initial population density, the number of alive cells grows exponentially (top row - deterministic-growth phase) or decreases exponentially until extinction (bottom row - no-growth phase). For intermediate population densities (2nd and 3rd rows - random-growth), the population is very sensitive to the stochastic transitions of very few alive cells (at ~300 h). Based on whether these cells stay alive without replicating, replicate, or die in the next time steps, the population can eventually either expand and grow exponentially or go extinct. b, The probability of replicating (blue) and the probability of dying (red) as a function of time for the same populations as in a. The probability of dying per unit time is fixed by temperature while the probability of replication is initially zero and increases over time as the alive cells always secrete glutathione (Fig. 5b). The probability of replicating quickly exceeds the probability of dying for high initial population densities (top row), leading to deterministic growth. For intermediate initial population densities (2nd and 3rd rows), the number of alive cells initially decreases over time as the probability of replicating continuously approaches - but stays smaller than - the probability of dying. Simultaneously, this decreasing pool of alive cells keeps secreting glutathione until, after ~300 h, the probability of replicating is very close to the probability of dying and very few alive cells are left in the population. Here, the probability of replicating either exceeds the probability of dying - leading to exponential growth - or remains smaller than the probability of dying - leading to extinction. This results in random-growth. For low initial population densities (bottom row), the probability of replicating remains well below the probability of dying. Here, the population goes extinct before the alive cells can secrete sufficient glutathione to increase the probability of replicating, leading to no growth.

Extended Data Fig. 4 A mutant strain that cannot synthesize glutathione detects glutathione secreted by wild-type yeasts at high temperatures (Related to Fig. 4e and Supplementary Fig. 11).

a, We constructed a mutant strain that could not synthesize glutathione by knocking out, in the wild-type strain, the GSH1 gene which is essential for glutathione biosynthesis (see “Mutant yeasts” in the Methods section). Glutathione has essential intracellular roles in yeast, so the Δgsh1-mutant can only grow in media that we supplement with glutathione40. To check this, we incubated starved the Δgsh1-mutant cells in SD-media to which we added 0 μM, 0.25 μM or 2.5 μM glutathione. These cells did not grow in medium without any glutathione (0 μM) but they grew in media with very small amounts of glutathione (i.e., more than 0.25 μM of extracellular glutathione). b, We used the Δgsh1-mutant strain to detect glutathione secreted by cells at high temperatures. We separated the growth media from cells grown at a fixed temperature by flowing the liquid cultures through 0.45μm-pore filters as previously described. We confirmed that there were no cells left behind in the filtered media by flowing the media through a flow cytometer. We then transplanted Δgsh1-mutant cells that were starved of glutathione into these filtered media at 30 OC. Subsequently, we then measured the resulting population densities over time in 30.0 OC. c-d, For example, we took the growth media from wild-type cells, just before growth at 39.2 OC (c) or during late log-phase growth at 30.0 OC (d). We then gave these filtered media to Δgsh1-cells and incubated them at 30.0 OC (green curves). As a control, we incubated populations of Δgsh1-cells at the same starting density in fresh media without any glutathione (grey curves). Only the media taken from cells incubated at high temperatures (39.2 OC) was able to induce growth of Δgsh1-cells. For all colors in each panel, there are n = 4 (a) or n = 3 (c, d) replicate populations. This result complements Supplementary Fig. 11, supporting our finding that wild-type cells secrete glutathione at micromolar concentrations at high temperatures (only above 36 OC).

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Supplementary Information

Supplementary Figs. 1–14 and text.

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Source data for Fig. 2a–f.

Source Data Fig. 3

Source data for Fig. 3b,d.

Source Data Fig. 4

Source data for Fig. 4b–f.

Source Data Fig. 6

Source data for Fig. 6a,c–e.

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Laman Trip, D.S., Youk, H. Yeasts collectively extend the limits of habitable temperatures by secreting glutathione. Nat Microbiol 5, 943–954 (2020). https://doi.org/10.1038/s41564-020-0704-2

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