Adaptive Roles ofSSY1andSIR3During Cycles of Growth and Starvation inSaccharomyces cerevisiaePopulations Enriched for Quiescent or Nonquiescent Cells

Abstract

Over its evolutionary history, Saccharomyces cerevisiae has evolved to be well-adapted to fluctuating nutrient availability. In the presence of sufficient nutrients, yeast cells continue to proliferate, but upon starvation haploid yeast cells enter stationary phase and differentiate into nonquiescent (NQ) and quiescent (Q) cells. Q cells survive stress better than NQ cells and show greater viability when nutrient-rich conditions are restored. To investigate the genes that may be involved in the differentiation of Q and NQ cells, we serially propagated yeast populations that were enriched for either only Q or only NQ cell types over many repeated growth–starvation cycles. After 30 cycles (equivalent to 300 generations), each enriched population produced a higher proportion of the enriched cell type compared to the starting population, suggestive of adaptive change. We also observed differences in each population’s fitness suggesting possible tradeoffs: clones from NQ lines were better adapted to logarithmic growth, while clones from Q lines were better adapted to starvation. Whole-genome sequencing of clones from Q- and NQ-enriched lines revealed mutations in genes involved in the stress response and survival in limiting nutrients (ECM21, RSP5, MSN1, SIR4, and IRA2) in both Q and NQ lines, but also differences between the two lines: NQ line clones had recurrent independent mutations affecting the Ssy1p-Ptr3p-Ssy5p (SPS) amino acid sensing pathway, while Q line clones had recurrent, independent mutations in SIR3 and FAS1. Our results suggest that both sets of enriched-cell type lines responded to common, as well as distinct, selective pressures.

Division of labour in the yeast: Saccharomyces cerevisiae

“…When a stationary phase population of haploid S. cerevisiae is starved of nutrients, a fraction of about 75% of cells exit the mitotic cycle and enter a ‘quiescent’ state (Q) (Allen et al ., ; Wloch‐Salamon et al ., ), which is physiologically similar to that seen in eukaryotic G 0 cells (Gray et al ., ; Valcourt et al ., ). The other cells in the population are non‐quiescent (NQ) and may continue proliferating.…”

“…Studies of experimentally evolved mutants with altered proportions of Q/NQ cells reveal that NQ‐rich cell‐lines are better adapted for exponential growth, while clones enriched for Q cells are better adapted to starvation. The ancestral strain, (75% Q and 25% NQ) outcompetes others in alternating environments, where cells are exposed to cycles of growth and starvation (Wloch‐Salamon et al ., ). Cooperation between Q and NQ cells therefore appears to be condition dependent, and was shown only during cycles of growth and starvation.…”

Yeast lines selected for non-quiescence show increased protein content

“…To investigate a genetic mechanism responsible for the observed phenotypic changes (increased NQ fraction as well as increase in protein content), we analyzed the spectrum of mutations acquired during Wloch-Salamon et al, 2017). We found 3 different mutations in the SSY1 gene (one in each experimental line), which suggests that these were independent events.…”

“…The experimental selection that we performed was described previously (D. M. Wloch-Salamon, Tomala, Aggeli, & Dunn, 2017). In brief, we used a derivative of the laboratory haploid strain s288C (Mat α, ura3::KanMX4) (F. A.…”

“…M. Wloch-Salamon et al, 2017). For the purpose of this project, we used sequences of seven clones: 2 clones isolated from each of the experimental t30 lines (1_SSY1c; 2_SSY1c; 3_SSY1c; 4_PTR3c; 5_SSY5c; 6_NO SPSc) and the ancestral clone (7_ancestral).…”