System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae
System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae
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DOI：
10.1534/genetics.110.120766
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发表时间：
2011-01-01
期刊：
影响因子：
3.3
通讯作者：
Botstein, David
中科院分区：
文献类型：
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作者：
Gresham, David;Boer, Viktor M.;Botstein, David
所有细胞的一个基本属性是能够退出活跃的细胞分裂并保持静止状态。对于单细胞微生物来说，这主要发生在营养匮乏的反应中。我们研究了酿酒酵母在饥饿的两种营养物质：磷酸盐或亮氨酸时生存的遗传要求。我们使用定量测序方法测量了混合种群中几乎所有非必需单倍体零酵母突变体的存活率，该方法基于独特的分子条形码的频率来估计每个突变体的丰度。饥饿的磷酸盐导致的种群半衰期为337小时，而饥饿的亮氨酸导致的半衰期为27.7小时。为了衡量个体突变体在每个种群中的存活率，我们开发了一个统计框架，解释了实验变异的多个来源。从突变强烈影响存活的基因的特性中，我们确定了在营养饥饿过程中影响存活的几个细胞过程的遗传证据，包括自噬、染色质重塑、mRNA加工和细胞骨架功能。此外，我们还发现了线粒体和过氧化物体功能是生存所必需的证据。我们的实验和分析方法代表了一种高效和定量的方法，以前所未有的分辨率表征遗传功能和网络，并识别出基因与环境的相互作用，这对解释酵母衰老和静止的研究具有重要意义。
An essential property of all cells is the ability to exit from active cell division and persist in a quiescent state. For single-celled microbes this primarily occurs in response to nutrient deprivation. We studied the genetic requirements for survival of Saccharomyces cerevisiae when starved for either of two nutrients: phosphate or leucine. We measured the survival of nearly all nonessential haploid null yeast mutants in mixed populations using a quantitative sequencing method that estimates the abundance of each mutant on the basis of frequency of unique molecular barcodes. Starvation for phosphate results in a population half-life of 337 hr whereas starvation for leucine results in a half-life of 27.7 hr. To measure survival of individual mutants in each population we developed a statistical framework that accounts for the multiple sources of experimental variation. From the identities of the genes in which mutations strongly affect survival, we identify genetic evidence for several cellular processes affecting survival during nutrient starvation, including autophagy, chromatin remodeling, mRNA processing, and cytoskeleton function. In addition, we found evidence that mitochondrial and peroxisome function is required for survival. Our experimental and analytical methods represent an efficient and quantitative approach to characterizing genetic functions and networks with unprecedented resolution and identified genotype-by-environment interactions that have important implications for interpretation of studies of aging and quiescence in yeast.