Abstract
Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. Here, we studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We performed pooled analysis of genotypes using molecular barcode sequencing (Bar‐seq) to test the role of ~4,000 gene deletion mutants and ~12,000 pairwise interactions between all non‐essential genes and the protein kinase genes TOR1,RIM15, and PHO85 in three different nutrient‐restricted conditions in both proliferative and quiescent cells. We detect up to 10‐fold more genetic interactions in quiescent cells than proliferative cells. We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro‐quiescence signal. The master regulator of quiescence, RIM15, shows distinct genetic interaction profiles in response to different starvation signals. However, vacuole‐related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome‐wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis.
Highlights
Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways
Cellular quiescence in yeast can be induced through a variety of nutrient deprivations, but whether establishment of a quiescent state in response to different starvation signals requires the same genetic factors and interactions is poorly understood
Double mutant libraries were constructed using genetic crosses between the ~4,800 non-essential gene deletion strains (Giaever et al 2002) and query strains deleted for one of three genes encoding the catalytic subunit of different regulatory protein kinases: TOR1, RIM15, and PHO85 (Table EV1 and Materials and Methods)
Summary
Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. We studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We detect up to 10-fold more genetic interactions in quiescent cells than proliferative cells We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro-quiescence signal. Vacuole-related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome-wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis
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