Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states
Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states
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DOI：
10.15252/msb.20199167
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发表时间：
2020-05
影响因子：
9.9
通讯作者：
Siyu Sun;A. Baryshnikova;Nathan Brandt;D. Gresham
中科院分区：
文献类型：
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作者：
Siyu Sun;A. Baryshnikova;Nathan Brandt;D. Gresham
真核细胞中的细胞生长和静止是由进化上保守的信号通路网络控制的。当细胞退出增殖生长并开始处于静止状态时，信号转导网络的作用是调节广泛的细胞过程和生理特性。信号网络如何对导致细胞周期退出和建立静止状态的不同信号做出反应，目前还知之甚少。在这里，我们研究了静止期细胞中信号通路的功能，利用全球遗传相互作用定位在真核细胞，酿酒酵母(发芽酵母)。我们使用分子条形码测序技术(Bar-seq)进行了基因分型的联合分析，以测试在三种不同的营养限制条件下，在增殖和静止细胞中，~4,000个基因缺失突变和~12,000个非必需基因与蛋白激酶基因TOR1、RIM15和PHO85之间的成对相互作用。我们在静止细胞中检测到的遗传交互作用是增殖细胞中的10倍。我们发现，个体基因效应和遗传交互作用特征都取决于特定的静息信号。静止期的主要调控因子RIM15对不同的饥饿信号表现出不同的遗传交互作用。然而，空泡相关功能与RIM15在不同的饥饿信号下表现出一致的遗传相互作用，这表明RIM15整合了不同的信号来维持静止细胞中的蛋白质动态平衡。我们的研究将全基因组遗传交互作用图谱扩展到其他条件和表型，并强调了上位性的条件性依赖。
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.