Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence.
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence.
复制标题
DOI：
10.1074/jbc.m110.157420
复制
发表时间：
2011-02-11
期刊：
影响因子：
--
通讯作者：
Castagnoli L
中科院分区：
文献类型：
--
作者：
Ferrari E;Tinti M;Costa S;Corallino S;Nardozza AP;Chatraryamontri A;Ceol A;Cesareni G;Castagnoli L
越来越多的证据表明，酪氨酸磷酸酶显示出对靶磷酸酪氨酸侧翼序列的内在酶促偏好。另一方面，底物在体内的选择是决定性的蛋白质相互作用网络中的酶-底物连接指导。我们在这里描述了一个系统范围的策略来推断蛋白质酪氨酸磷酸酶的生理底物。在这里，我们整合，贝叶斯模型，蛋白质组广泛的证据，在体外底物的偏好，确定了一种新的高密度肽芯片技术，和“亲密”的蛋白质相互作用网络。这允许对人PTP 1B磷酸酶的候选底物进行排序。最终，使用多种体外和体内方法来验证预测，即五种高级底物PLC-γ1、Gab 1、SHP 2、EGFR和SHP 1的酪氨酸磷酸化水平确实受到PTP 1B的特异性调节。此外，我们证明了PTP 1B介导的Gab 1去磷酸化对其EGF诱导的与磷酸酶SHP 2的关联产生负面影响。这种信号复合物的解离伴随着ERK MAP激酶磷酸化和活化的减少。
There is growing evidence that tyrosine phosphatases display an intrinsic enzymatic preference for the sequence context flanking the target phosphotyrosines. On the other hand, substrate selection in vivo is decisively guided by the enzyme-substrate connectivity in the protein interaction network. We describe here a system wide strategy to infer physiological substrates of protein-tyrosine phosphatases. Here we integrate, by a Bayesian model, proteome wide evidence about in vitro substrate preference, as determined by a novel high-density peptide chip technology, and “closeness” in the protein interaction network. This allows to rank candidate substrates of the human PTP1B phosphatase. Ultimately a variety of in vitro and in vivo approaches were used to verify the prediction that the tyrosine phosphorylation levels of five high-ranking substrates, PLC-γ1, Gab1, SHP2, EGFR, and SHP1, are indeed specifically modulated by PTP1B. In addition, we demonstrate that the PTP1B-mediated dephosphorylation of Gab1 negatively affects its EGF-induced association with the phosphatase SHP2. The dissociation of this signaling complex is accompanied by a decrease of ERK MAP kinase phosphorylation and activation.