Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment.
Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment.
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DOI：
10.1371/journal.pgen.1003972
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发表时间：
2013-11
期刊：
影响因子：
4.5
通讯作者：
Sherlock G
中科院分区：
文献类型：
--
作者：
Kvitek DJ;Sherlock G
分子信号网络在生命中无处不在，并且可能进化为允许生物体在动态环境中感知和响应环境变化。很少有关于信号网络可有可无的例子，而且目前还不清楚它们是否是高度适应的生物系统的基本特征。在这里，我们表明，信号网络功能进行健身成本在酵母在恒定的环境中不断演变。我们对重复进化实验进行了全基因组、全种群Illumina测序，发现在恒定环境中适应性进化的主要主题是负责调节对环境扰动反应的信号网络的破坏。超过一半的突变发生在调节生长控制的三个主要信号网络中：葡萄糖信号，Ras/cAMP/PKA和HOG。这导致在实验中可重复的环境敏感性的损失。然而，适应性克隆在饥饿条件下表现出降低的生存能力，这表明了进化的权衡。这些突变在具有恒定和可预测的营养供应的环境中是有益的，可能是因为它们导致组成性生长，但在营养供应不恒定的环境中降低适应性。我们的研究结果是进化短视本质的一个明显例子：在恒定环境中失去环境敏感性在短期内是适应性的，但如果环境发生变化，则是适应不良。当一个生物种群面临选择压力时，例如营养有限，随机出现的突变可能会给携带该突变的个体带来适应性益处。如果该个体在从种群中消失之前繁殖，则该突变的频率可能会增加。随着时间的推移，许多有益的突变将出现在一个大的群体中，但很少有高分辨率的实验跟踪这种突变在不断发展的群体中的频率。我们在有限糖含量的恒定环境中进化了面包酵母的种群，然后使用DNA测序来识别种群中至少达到1%频率的突变，并随着时间的推移跟踪它们。我们在三个实验中鉴定了120个突变，并确定获得有益突变的基因和途径在实验中基本上是可重复的，并且许多突变导致通常感知环境变化的信号通路的丢失，从而使细胞能够做出适当的反应。当这些突变细胞面对不确定的环境时，突变被证明是有害的。环境感知在恒定的环境中必须承担适应性成本，但在变化的环境中是必不可少的。
Molecular signaling networks are ubiquitous across life and likely evolved to allow organisms to sense and respond to environmental change in dynamic environments. Few examples exist regarding the dispensability of signaling networks, and it remains unclear whether they are an essential feature of a highly adapted biological system. Here, we show that signaling network function carries a fitness cost in yeast evolving in a constant environment. We performed whole-genome, whole-population Illumina sequencing on replicate evolution experiments and find the major theme of adaptive evolution in a constant environment is the disruption of signaling networks responsible for regulating the response to environmental perturbations. Over half of all identified mutations occurred in three major signaling networks that regulate growth control: glucose signaling, Ras/cAMP/PKA and HOG. This results in a loss of environmental sensitivity that is reproducible across experiments. However, adaptive clones show reduced viability under starvation conditions, demonstrating an evolutionary tradeoff. These mutations are beneficial in an environment with a constant and predictable nutrient supply, likely because they result in constitutive growth, but reduce fitness in an environment where nutrient supply is not constant. Our results are a clear example of the myopic nature of evolution: a loss of environmental sensitivity in a constant environment is adaptive in the short term, but maladaptive should the environment change. When a population of organisms is faced with a selective pressure, such as a limiting nutrient, mutations that arise randomly may confer a fitness benefit on the individual carrying that mutation. If that individual reproduces before it is lost from the population, the frequency of that mutation may increase. Over time, many beneficial mutations will arise in a large population, but there are few high resolution experiments tracking the frequency of such mutations in an evolving population. We evolved populations of the baker's yeast in a constant environment in the presence of limiting amounts of sugar, and then used DNA sequencing to identify mutations that reached at least a 1% frequency in the population, and tracked them over time. We identified 120 mutations over three experiments, and determined that the genes and pathways that had gained beneficial mutations were largely reproducible across experiments, and that many of the mutations led to the loss of signaling pathways that usually sense a changing environment, allowing the cell to respond appropriately. When these mutant cells were faced with uncertain environments, the mutations proved to be deleterious. Environmental sensing must carry a fitness cost in a constant environment, but is essential in a changing one.
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影响因子：
64.8
作者：
Greaves, Mel;Maley, Carlo C.
通讯作者：
Maley, Carlo C.
影响因子：
3.3
作者：
Hall, David W.;Joseph, Sarah B.
通讯作者：
Joseph, Sarah B.
影响因子：
64.8
作者：
Cooper, VS;Lenski, RE
通讯作者：
Lenski, RE
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y