Mardones Wladimir, Villarroel Carlos A, Abarca Valentina, Urbina Kamila, Peña Tomás A, Molinet Jennifer, Nespolo Roberto F, Cubillos Francisco A
Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.
Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile.
Microb Biotechnol. 2022 Mar;15(3):967-984. doi: 10.1111/1751-7915.13803. Epub 2021 Mar 23.
Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time-course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off-flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in 'fast motion' in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
尽管人类驯化综合征下生物体进化的典型基因组和表型变化是快速进化的教科书式例子，但支撑这些变化的分子过程仍知之甚少。用于酿造的驯化酵母就是典型例子，在选择作用下，其在几代内就实现了较短的世代时间以及较大的表型和基因组可塑性。为了通过实验模拟拉格酵母的驯化过程，我们创建了一个由多个真贝氏酵母基因型组成的遗传复杂（随机交配）人工群体，真贝氏酵母是拉格酵母的亲本之一。然后，我们在10个重复群体中，在高乙醇浓度下施加恒定选择机制，持续260代（6个月），并将它们与仅暴露于葡萄糖的传代对照进行比较。传代群体在乙醇中的生长速率表现出60%的选择差异，这主要是由一个单一谱系（CL248.1）的增殖所导致的，该谱系竞争性地取代了所有其他克隆。有趣的是，这一结果并不需要整个适应过程的时间，因为在第120代时，四个谱系就垄断了培养物。测序表明，所有传代品系中都产生了新生遗传变异，包括单核苷酸多态性、非整倍体、插入缺失和易位。此外，不同的传代群体表现出类似驯化综合征的相关反应：基因组重排、更快的发酵速率、更低的酚类异味产生以及更低的挥发性化合物复杂性。在麦芽汁中的表达谱分析揭示了与蛋氨酸代谢、絮凝、胁迫耐受性和二次生长转变相关基因的表达水平发生了变化，这可能有助于进化群体对更高乙醇和发酵胁迫的耐受性。我们的研究表明，实验进化可以在野生酵母中“快速”重建酿造驯化过程，并且还为研究复杂群体适应过程的遗传学提供了一个强大工具。
