Gene-dependent cell death in yeast

Abstract

Caspase-dependent apoptotic cell death has been extensively studied in cultured cells and during embryonic development, but the existence of analogous molecular pathways in single-cell species is uncertain. This has reduced enthusiasm for applying the advanced genetic tools available for yeast to study cell death regulation. However, partial characterization in mammals of additional genetically encoded cell death mechanisms, which lead to a range of dying cell morphologies and necrosis, suggests potential applications for yeast genetics. In this light, we revisited the topic of gene-dependent cell death in yeast to determine the prevalence of yeast genes with the capacity to contribute to cell-autonomous death. We developed a rigorous strategy by allowing sufficient time for gene-dependent events to occur, but insufficient time to evolve new populations, and applied this strategy to the Saccharomyces cerevisiae gene knockout collection. Unlike sudden heat shock, a ramped heat stimulus delivered over several minutes with a thermocycler, coupled with assessment of viability by automated counting of microscopic colonies revealed highly reproducible gene-specific survival phenotypes, which typically persist under alternative conditions. Unexpectedly, we identified over 800 yeast knockout strains that exhibit significantly increased survival following insult, implying that these genes can contribute to cell death. Although these death mechanisms are yet uncharacterized, this study facilitates further exploration.

Genome-wide identification of genes involved in the positive and negative regulation of acetic acid-induced programmed cell death in Saccharomyces cerevisiae

“…Number of genes with a phenotype in each of these studies and that displayed increased susceptibility (A) or resistance (B) to acetic acid in our study. Genes with common phenotypes between the studies of Teng et al [45], Mira et al [16] and Kawahata et al [15] are not evidenced in the representation. The numbers in the centre of “Our results” circles represent the number of genes found exclusively in our screen.…”

Cell death in genome evolution

“…Cell death screens of the entire ~5,000 unique knockout strains in the yeast knockout collection revealed over 800 candidate genes, when deleted, result in two-fold or better survival following exposure to a heat ramp stimulus, or to acetate concentrations compared to the wild type strains [2, 76]. Based on 1-2 month evolution experiments, cell death mechanisms are required for long-term survival of single-cell species, for example, to reduce the population to a size that is sustainable on the available resources [77].…”

“…This assay is based on the viability of yeast knockout strains after treatment with precisely regulated heat ramp stimuli (a condition mild enough to allow time for gene-dependent cell death to occur but prior to adaptation), regardless of the cell morphologies during the dying process [80]. By applying this assay to the yeast knockout collection, we found unexpectedly that many gene knockout strains (~40%) are more resistant to cell death compared to the parental wild type strain [2]. This suggested that many genes can contribute to cell suicide when the environmental temperature is increased gradually [2].…”

“…By applying this assay to the yeast knockout collection, we found unexpectedly that many gene knockout strains (~40%) are more resistant to cell death compared to the parental wild type strain [2]. This suggested that many genes can contribute to cell suicide when the environmental temperature is increased gradually [2]. We also compared different metabolic states when death was induced by heat treatment versus acidic acid, the primary organic acid that accumulates in overgrown cultures of yeast.…”

“…New strategies to test every non-essential gene of Saccharomyces cerevisiae for the ability to promote cell death revealed surprising answers. Several hundred different genes, when deleted individually, greatly increase cell survival [2]. However, death-resistance for many of these knockout strains may be due to acquired secondary mutations.…”