Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast.
Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast.
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基因与环境的相互作用影响酵母中基因拷贝数变异的适应成本。
DOI：
10.1101/2023.05.11.540375
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Gasch,AudreyP
中科院分区：
文献类型：
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作者：
Robinson,DeElegant;Vanacloig-Pedros,Elena;Cai,Ruoyi;Place,Michael;Hose,James;Gasch,AudreyP
基因拷贝数的变化可以改变基因表达并影响下游表型；因此，如果收益大于成本，拷贝数变异（CNV）为快速进化提供了一条途径。我们最近发现遗传背景显著影响酵母细胞对基因过表达（OE）的反应，揭示了在普通花园环境中，CNV的适应度成本会随着遗传背景的变化而发生很大变化。但在基因组尺度上，CNV耐受性和环境之间的相互作用仍未被探索。在氯化钠（NaCl）胁迫下，测定了4株遗传差异明显的酿酒酵母（Saccharomyces cerevisiae）菌株对OE基因的耐受性。在NaCl胁迫下通常有害的OE基因重现了在标准条件下通常有害的OE基因。然而，NaCl胁迫揭示了菌株对OE基因反应的新差异。西非菌株NCYC3290和北美橡木分离株YPS128对NaCl胁迫的敏感性高于葡萄园菌株BC187和实验室菌株BY4743。NCYC3290和YPS128对OE基因的敏感性最高。虽然大多数基因是有害的，但当过度表达时，有数百个基因是有益的，值得注意的是，这些影响大多是菌株特异性的。对NaCl敏感的菌株之间共享的有益基因很少，这暗示了它们对NaCl敏感的机制差异。转录组学分析表明，菌株之间存在潜在的脆弱性和耐受性，并指出钠输出泵的天然CNV可能有助于菌株对其他基因的OE产生特异性反应。我们的研究结果揭示了对基因CNV的反应中广泛的菌株-环境相互作用，这对逆境下CNV依赖的进化途径的可及性提出了重要的启示。
Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation (CNV) provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene over-expression (OE), revealing that the fitness costs of CNV can vary substantially with genetic background in a common-garden environment. But the interplay between CNV tolerance and environment remains unexplored on a genomic scale. Here we measured the tolerance to gene OE in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride (NaCl) stress. OE genes that are commonly deleterious during NaCl stress recapitulated those commonly deleterious under standard conditions. However, NaCl stress uncovered novel differences in strain responses to gene OE. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to NaCl stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to gene OE. Although most genes were deleterious, hundreds were beneficial when over-expressed, Remarkably, most of these effects were strain specific. Few beneficial genes were shared between the NaCl-sensitive isolates, implicating mechanistic differences behind their NaCl sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural CNV of a sodium export pump that likely contributes to strain-specific responses to OE of other genes. Our results reveal extensive strain-by-environment interaction in the response to gene CNV, raising important implications for the accessibility of CNV-dependent evolutionary routes under times of stress.