MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P
Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
J Proteome Res. 2020 Aug 7;19(8):3405-3417. doi: 10.1021/acs.jproteome.0c00253. Epub 2020 Jul 13.
To cope with sudden changes in the external environment, the budding yeast orchestrates a multifaceted response that spans many levels of physiology. Several studies have interrogated the transcriptome response to endoplasmic reticulum (ER) stress and the role of regulators such as the Ire1 kinase and Hac1 transcription factors. However, less is known about responses to ER stress at other levels of physiology. Here, we used quantitative phosphoproteomics and computational network inference to uncover the yeast phosphoproteome response to the reducing agent dithiothreitol (DTT) and the upstream signaling network that controls it. We profiled wild-type cells and mutants lacking or MAPK kinases and , before and at various times after DTT treatment. In addition to revealing downstream targets of these kinases, our inference approach predicted new regulators in the DTT response, including cell-cycle regulator Cdc28 and osmotic-response kinase Rck2, which we validated computationally. Our results also revealed similarities and surprising differences in responses to different stress conditions, especially in the response of protein kinase A targets. These results have implications for the breadth of signaling programs that can give rise to common stress response signatures.
为应对外部环境的突然变化，出芽酵母会协调一系列多方面的反应，这些反应涉及多个生理层面。多项研究探讨了转录组对内质网（ER）应激的反应以及诸如Ire1激酶和Hac1转录因子等调节因子的作用。然而，对于其他生理层面的内质网应激反应了解较少。在此，我们运用定量磷酸化蛋白质组学和计算网络推断方法，来揭示酵母磷酸化蛋白质组对还原剂二硫苏糖醇（DTT）的反应以及控制该反应的上游信号网络。我们在DTT处理之前及之后的不同时间点，对野生型细胞以及缺乏丝裂原活化蛋白激酶（MAPK）激酶Ste11和Ste7的突变体进行了分析。除了揭示这些激酶的下游靶点外，我们的推断方法还预测了DTT反应中的新调节因子，包括细胞周期调节因子Cdc28和渗透反应激酶Rck2，我们通过计算对其进行了验证。我们的结果还揭示了对不同应激条件反应的相似性和惊人差异，特别是在蛋白激酶A靶点的反应方面。这些结果对于能够产生共同应激反应特征的信号程序的广度具有启示意义。
