The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression, our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind. Across all model organisms, the causal mutations have been discovered for only a handful of gene expression adaptations, and even for these, mechanistic details (e.g. the trans-regulatory factors involved) have not been determined. We previously reported a polygenic gene expression adaptation involving down-regulation of the ergosterol biosynthesis pathway in the budding yeast Saccharomyces cerevisiae. Here we investigate the molecular mechanism of a cis-acting mutation affecting a member of this pathway, ERG28. We show that the causal mutation is a two-base deletion in the promoter of ERG28 that strongly reduces the binding of two transcription factors, Sok2 and Mot3, thus abolishing their regulation of ERG28. This down-regulation increases resistance to a widely used antifungal drug targeting ergosterol, similar to mutations disrupting this pathway in clinical yeast isolates. The identification of the causal genetic variant revealed that the selection likely occurred after the deletion was already present at high frequency in the population, rather than when it was a new mutation. These results provide a detailed view of the molecular mechanism of a cis-regulatory adaptation, and underscore the importance of this view to our understanding of evolution at the molecular level.尽管目前我们在检测涉及基因表达顺式调控（cis-regulation）的适应性进化方面已取得一定进展，但对于这些适应性进化背后的分子机制的认知仍远远滞后。在所有模式生物中，仅针对少数基因表达适应性事件成功鉴定出因果突变；即便针对这些已确定突变的事件，其背后的机制细节（例如所涉及的反式调控（trans-regulation）因子）仍未明确。我们此前曾在酿酒酵母（Saccharomyces cerevisiae）中报道过一项涉及麦角固醇生物合成通路下调的多基因基因表达适应性事件。本文针对该通路中的成员基因ERG28的顺式作用（cis-acting）突变的分子机制展开研究。我们证实，该因果突变是ERG28启动子（promoter）区域的两处碱基缺失，该突变会大幅削弱转录因子Sok2与Mot3的结合能力，从而消除二者对ERG28的调控作用。这种下调作用可提升细胞对一款广泛使用的靶向麦角固醇的抗真菌药物（antifungal drug）的抗性，这与临床酵母分离株中破坏该通路的突变所产生的表型一致。对该因果遗传变异的鉴定结果显示，此次适应性选择大概率发生在该缺失突变已在种群中达到高频率之后，而非发生于该突变刚出现的阶段。本研究详细阐明了一项顺式调控适应性进化的分子机制，同时凸显了这类机制解析对于我们理解分子层面进化过程的重要意义。