Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway.
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway.
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DOI：
10.1007/s00239-022-10079-9
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发表时间：
2023-02
影响因子：
3.9
通讯作者：
中科院分区：
文献类型：
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半乳糖是一种次级可发酵糖，需要特定的调节和结构基因来进行同化，这些基因受到葡萄糖分解代谢的抑制。当缺乏葡萄糖时，分解代谢的抑制作用减弱，结构上的半乳糖基因被完全激活。在酿酒酵母中，GAL途径在半乳糖存在的环境中处于选择状态。然而，在实验室进化实验中，对于作为唯一碳源的半乳糖的长期繁殖，其适应策略尚不清楚。在这里，我们使用48个二倍体酿酒酵母种群进行了4000代的进化实验，以研究半乳糖的适应性。我们表明，在半乳糖进化的种群中，适应度的增加比以葡萄糖为唯一碳源的相同进化的种群更大。对96个进化克隆的全基因组测序显示，候选选择目标中反复出现从头开始的单核苷酸突变、拷贝数变异和倍性变化。我们发现，大多数改善半乳糖适合性的突变都位于典型的GAL途径之外。对候选选择目标SEC23和IRA1中特定进化等位基因的重建表明，与葡萄糖相比，半乳糖的适合度显著增加。此外，我们的进化群体中的大多数(28/46；61%)固定在染色体上的非整倍体，这表明平行的适应性扩增。最后，我们发现，与先前的葡萄糖进化相比，我们的葡萄糖进化谱系中染色体外成分的损失更大。总的来说，这些数据加深了我们对进化压力的理解，这些压力推动我们适应不那么受欢迎的碳源。网上版载有补充材料，可在10.1007/s00239-022-10079-9查阅。
Galactose is a secondary fermentable sugar that requires specific regulatory and structural genes for its assimilation, which are under catabolite repression by glucose. When glucose is absent, the catabolic repression is attenuated, and the structural GAL genes are fully activated. In Saccharomyces cerevisiae, the GAL pathway is under selection in environments where galactose is present. However, it is unclear the adaptive strategies in response to long-term propagation in galactose as a sole carbon source in laboratory evolution experiments. Here, we performed a 4,000-generation evolution experiment using 48 diploid Saccharomyces cerevisiae populations to study adaptation in galactose. We show that fitness gains were greater in the galactose-evolved population than in identically evolved populations with glucose as a sole carbon source. Whole-genome sequencing of 96 evolved clones revealed recurrent de novo single nucleotide mutations in candidate targets of selection, copy number variations, and ploidy changes. We find that most mutations that improve fitness in galactose lie outside of the canonical GAL pathway. Reconstruction of specific evolved alleles in candidate target of selection, SEC23 and IRA1, showed a significant increase in fitness in galactose compared to glucose. In addition, most of our evolved populations (28/46; 61%) fixed aneuploidies on Chromosome VIII, suggesting a parallel adaptive amplification. Finally, we show greater loss of extrachromosomal elements in our glucose-evolved lineages compared with previous glucose evolution. Broadly, these data further our understanding of the evolutionary pressures that drive adaptation to less-preferred carbon sources. The online version contains supplementary material available at 10.1007/s00239-022-10079-9.
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DOI：
10.1016/j.tig.2021.08.013
发表时间：
2022-01
期刊：
Trends in genetics : TIG
影响因子：
--
作者：
Harrison MC;LaBella AL;Hittinger CT;Rokas A
通讯作者：
Rokas A
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
DOI：
10.1093/bioinformatics/btr670
发表时间：
2012-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Boeva V;Popova T;Bleakley K;Chiche P;Cappo J;Schleiermacher G;Janoueix-Lerosey I;Delattre O;Barillot E
通讯作者：
Barillot E
影响因子：
--
作者：
Fendt SM;Sauer U
通讯作者：
Sauer U
影响因子：
3.3
作者：
Aggeli, Dimitra;Marad, Daniel A.;Lang, Gregory, I
通讯作者：
Lang, Gregory, I