Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
Sci Signal. 2010 Dec 21;3(153):rs4. doi: 10.1126/scisignal.2001182.
The phosphorylation and dephosphorylation of proteins by kinases and phosphatases constitute an essential regulatory network in eukaryotic cells. This network supports the flow of information from sensors through signaling systems to effector molecules and ultimately drives the phenotype and function of cells, tissues, and organisms. Dysregulation of this process has severe consequences and is one of the main factors in the emergence and progression of diseases, including cancer. Thus, major efforts have been invested in developing specific inhibitors that modulate the activity of individual kinases or phosphatases; however, it has been difficult to assess how such pharmacological interventions would affect the cellular signaling network as a whole. Here, we used label-free, quantitative phosphoproteomics in a systematically perturbed model organism (Saccharomyces cerevisiae) to determine the relationships between 97 kinases, 27 phosphatases, and more than 1000 phosphoproteins. We identified 8814 regulated phosphorylation events, describing the first system-wide protein phosphorylation network in vivo. Our results show that, at steady state, inactivation of most kinases and phosphatases affected large parts of the phosphorylation-modulated signal transduction machinery-and not only the immediate downstream targets. The observed cellular growth phenotype was often well maintained despite the perturbations, arguing for considerable robustness in the system. Our results serve to constrain future models of cellular signaling and reinforce the idea that simple linear representations of signaling pathways might be insufficient for drug development and for describing organismal homeostasis.
蛋白质的磷酸化和去磷酸化是真核细胞中一个重要的调控网络，由激酶和磷酸酶来完成。这个网络支持着信息从传感器传递到效应分子的过程，最终驱动细胞、组织和生物体的表型和功能。这个过程的失调会产生严重的后果，是疾病（包括癌症）发生和发展的主要因素之一。因此，人们投入了大量的努力来开发特异性的抑制剂，以调节单个激酶或磷酸酶的活性；然而，评估这种药理学干预如何影响整个细胞信号网络一直具有挑战性。在这里，我们使用无标记、定量磷酸蛋白质组学在一个系统扰动的模式生物（酿酒酵母）中，确定了 97 种激酶、27 种磷酸酶和 1000 多种磷酸化蛋白质之间的关系。我们鉴定了 8814 个受调控的磷酸化事件，描述了第一个体内全系统蛋白质磷酸化网络。我们的结果表明，在稳定状态下，大多数激酶和磷酸酶的失活会影响到大部分磷酸化调节的信号转导机制，而不仅仅是直接的下游靶点。尽管存在干扰，观察到的细胞生长表型通常仍能很好地维持，这表明该系统具有相当的稳健性。我们的结果有助于约束未来的细胞信号模型，并强化了这样一种观点，即信号通路的简单线性表示可能不足以进行药物开发和描述生物体的内稳态。
