Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination.
Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination.
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在波动氮饥饿下适应的途径：酿酒酵母自适应突变的光谱是由逆转座子和微型学介导的重组塑造的。
DOI：
10.1371/journal.pgen.1010747
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发表时间：
2023-05
期刊：
影响因子：
4.5
通讯作者：
中科院分区：
文献类型：
--
作者：
有许多机制引起基因组变化：虽然点突变经常在基因组分析中被强调，但进化作用于许多其他类型的遗传变化，这些变化可能导致不那么微妙的扰动。染色体结构、DNA拷贝数和新型转座子插入的变化都产生了大的基因组变化，这对表型和适应性产生了相应的巨大影响。在这项研究中，我们调查了适应性突变的频谱，出现在一个人口在不断波动的氮条件下。我们特别对比这些适应性等位基因和突变机制，创造他们，适应机制下批量葡萄糖限制和低，非波动氮条件下的恒定选择，以解决选择动力学是否以及如何影响进化适应的分子机制。我们观察到，反转录转座子活动占了大量的适应性事件，沿着微同源介导的插入，缺失和基因转换机制。除了在遗传筛选中经常利用的功能等位基因的丧失之外，我们还鉴定了推定的功能等位基因的获得和通过迄今尚不清楚的机制起作用的等位基因。总的来说，我们的研究结果强调，选择（波动与非波动）的应用方式也会影响适应，就像选择压力（氮与葡萄糖）本身一样。波动的环境可以激活不同的突变机制，从而相应地形成适应性事件。实验进化，它允许更广泛的适应性事件进行评估，因此是一种补充的方法，既经典的遗传筛选和自然变异的研究，以表征基因型表型健身地图。进化的一个主要驱动力是适应性突变的发生和随后的选择，这使得生物体更适合特定的环境。虽然适应性突变通常是点突变，如错义或无义突变，但还有许多其他类型的突变。在这里，我们发现，反转录转座事件，其中一个反转录转座子，使自己在基因组的其他地方的新副本，是频繁的酵母繁殖时，连续分批转移培养基中限制氮。此外，我们发现许多这样的事件是自适应的，并表明，逆转录转座的速率增加，在氮限制的培养基相比，葡萄糖限制的培养基，特别是当细胞增殖的串行批量转移。然而，当细胞在氮限制培养基中连续培养时，我们没有看到有益的逆转录转座事件的证据。我们的研究结果强调，选择（波动与非波动）的应用方式也会影响适应，就像选择压力（氮与葡萄糖）本身一样。
There are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in chromosome structure, DNA copy number, and novel transposon insertions all create large genomic changes, which can have correspondingly large impacts on phenotypes and fitness. In this study we investigate the spectrum of adaptive mutations that arise in a population under consistently fluctuating nitrogen conditions. We specifically contrast these adaptive alleles and the mutational mechanisms that create them, with mechanisms of adaptation under batch glucose limitation and constant selection in low, non-fluctuating nitrogen conditions to address if and how selection dynamics influence the molecular mechanisms of evolutionary adaptation. We observe that retrotransposon activity accounts for a substantial number of adaptive events, along with microhomology-mediated mechanisms of insertion, deletion, and gene conversion. In addition to loss of function alleles, which are often exploited in genetic screens, we identify putative gain of function alleles and alleles acting through as-of-yet unclear mechanisms. Taken together, our findings emphasize that how selection (fluctuating vs. non-fluctuating) is applied also shapes adaptation, just as the selective pressure (nitrogen vs. glucose) does itself. Fluctuating environments can activate different mutational mechanisms, shaping adaptive events accordingly. Experimental evolution, which allows a wider array of adaptive events to be assessed, is thus a complementary approach to both classical genetic screens and natural variation studies to characterize the genotype-to-phenotype-to-fitness map. A major driver of evolution is the occurrence and subsequent selection of adaptive mutations, which make an organism more fit in a given environment. While adaptive mutations are often point mutations, such as missense or nonsense mutations, there are many other types of mutation. Here we find that retrotransposition events, whereby a retrotransposon makes a new copy of itself elsewhere in the genome, are frequent when yeast are propagated by serial batch transfer in media with limiting nitrogen. Furthermore, we find many such events are adaptive, and show that the rate of retrotransposition is increased in nitrogen limited media compared to glucose limited media specifically when cells are propagated by serial batch transfer. However, we see no evidence of beneficial retrotransposition events when cells are propagated in nitrogen limited media in continuous culture. Our findings emphasize that how selection (fluctuating vs. non-fluctuating) is applied also shapes adaptation, just as the selective pressure (nitrogen vs. glucose) does itself.
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影响因子：
11.3
作者：
Conrad M;Schothorst J;Kankipati HN;Van Zeebroeck G;Rubio-Texeira M;Thevelein JM
通讯作者：
Thevelein JM
影响因子：
3.3
作者：
Ahn, Hyo Won;Tucker, Jessica M.;Garfinkel, David J.
通讯作者：
Garfinkel, David J.
影响因子：
5.3
作者：
BOEKE, JD;STYLES, CA;FINK, GR
通讯作者：
FINK, GR
DOI：
10.1007/bf00332411
发表时间：
1989-09-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
BRADSHAW, VA;MCENTEE, K
通讯作者：
MCENTEE, K
DOI：
10.1073/pnas.88.3.936
发表时间：
1991-02-01
影响因子：
11.1
作者：
CURCIO, MJ;GARFINKEL, DJ
通讯作者：
GARFINKEL, DJ