Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire.
Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire.
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DOI：
10.1371/journal.pcbi.1005869
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发表时间：
2017-11
影响因子：
4.3
通讯作者：
Wolf DA
中科院分区：
文献类型：
--
作者：
Straube R;Shah M;Flockerzi D;Wolf DA
Cullin-RING泛素连接酶（CRL）催化底物的泛素化，其中许多底物被26 S蛋白酶体降解。它们的模块化结构使得能够通过可交换的底物受体识别多种底物，所述底物受体以高亲和力竞争性地结合到cullin支架上。由于这些相互作用的可塑性，鉴于底物负荷的变化，细胞如何保持灵活的CRL库仍存在不确定性。基于一系列的体内和体外研究，不同的研究小组提出底物受体的交换是由一种名为Cand 1的蛋白质交换因子介导的。在这里，我们进行了数学建模，以提供这一假设的定量基础。首先，我们表明，Cand 1的交换活性必然导致高连接酶活性和快速受体交换之间的权衡。支持测量，我们认为，这种权衡产生一个最佳的Cand 1浓度在细胞中的时间尺度为基板退化变得最小。在第二步中，我们通过模拟表明，（i）基板偏置的CRL库导致优先组装的连接酶的基板是可用的和（ii）在结合亲和力或基板受体丰度的差异创建一个时间层次的降解基板。最后，我们比较了Cand 1介导的交换周期与缺乏Cand 1的替代架构，这表明如果底物受体以随机顺序结合底物和cullin支架，则具有交换因子的系统的优越性。总之，我们的研究结果提供了一般的分子交换系统的操作制度的限制，并建议Cand 1赋予CRL网络的“按需”系统的属性，允许细胞动态地调整其CRL库波动基板丰度。Cullin-RING泛素连接酶（CRL）是多亚基蛋白复合物，其中可交换底物受体（SR）在Cullin支架上组装以介导多种底物的泛素化和随后的降解。在人类中，有数百种不同的CRL，可能有数千种底物。由于cullin-SR相互作用的高亲和力，细胞如何保持对整个SR库进行采样的灵活性以匹配波动的底物负荷长期以来一直是一个谜。最近的实验表明，不同SR的交换是由一种新的蛋白质交换因子（Cand 1）介导的。然而，Cand 1作为CRL活性的启动子的建议的生化功能仍然难以调和与以前的报道Cand 1作为体外CRL活性的抑制剂。在这里，我们表明，这两个发现是不矛盾的，但交换活性的Cand 1必然导致高连接酶活性和快速受体交换之间的权衡，这使我们预测一个最佳的Cand 1浓度和时间层次的底物降解。我们的研究结果支持这样的观点，Cand 1赋予CRL网络的灵活性的“按需”系统的相对CRL丰度取决于基板的可用性。
Cullin-RING ubiquitin ligases (CRLs) catalyze the ubiquitylation of substrates many of which are degraded by the 26S proteasome. Their modular architecture enables recognition of numerous substrates via exchangeable substrate receptors that competitively bind to a cullin scaffold with high affinity. Due to the plasticity of these interactions there is ongoing uncertainty how cells maintain a flexible CRL repertoire in view of changing substrate loads. Based on a series of in vivo and in vitro studies, different groups proposed that the exchange of substrate receptors is mediated by a protein exchange factor named Cand1. Here, we have performed mathematical modeling to provide a quantitative underpinning of this hypothesis. First we show that the exchange activity of Cand1 necessarily leads to a trade-off between high ligase activity and fast receptor exchange. Supported by measurements we argue that this trade-off yields an optimal Cand1 concentration in cells where the time scale for substrate degradation becomes minimal. In a second step we show through simulations that (i) substrates bias the CRL repertoire leading to preferential assembly of ligases for which substrates are available and (ii) differences in binding affinities or substrate receptor abundances create a temporal hierarchy for the degradation of substrates. Finally, we compare the Cand1-mediated exchange cycle with an alternative architecture lacking Cand1 which indicates superiority of a system with exchange factor if substrate receptors bind substrates and the cullin scaffold in a random order. Together, our results provide general constraints for the operating regimes of molecular exchange systems and suggest that Cand1 endows the CRL network with the properties of an “on demand” system allowing cells to dynamically adjust their CRL repertoire to fluctuating substrate abundances. Cullin-RING ubiquitin ligases (CRLs) are multisubunit protein complexes where exchangeable substrate receptors (SRs) assemble on a cullin scaffold to mediate ubiquitylation and subsequent degradation of a large variety of substrates. In humans there are hundreds of different CRLs having potentially thousands of substrates. Due to the high affinity of cullin-SR interactions, it has long been a mystery how cells would maintain flexibility to sample the entire SR repertoire in order to match fluctuating substrate loads. Recent experiments indicate that the exchange of different SRs is mediated by a novel protein exchange factor (Cand1). However, the proposed biochemical function of Cand1 as a promoter of CRL activity remained difficult to reconcile with previous reports of Cand1 acting as an inhibitor of CRL activity in vitro. Here we show that these two findings are not contradictory, but that the exchange activity of Cand1 necessarily leads to a trade-off between high ligase activity and fast receptor exchange which leads us to predict an optimal Cand1 concentration and a temporal hierarchy for substrate degradation. Our results support the view that Cand1 endows the CRL network with the flexibility of an “on demand” system where relative CRL abundances are dictated by substrate availability.
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影响因子：
16
作者：
Saha, Anjanabha;Deshaies, Raymond J.
通讯作者：
Deshaies, Raymond J.
影响因子：
64.5
作者：
Duda, David M.;Borg, Laura A.;Scott, Daniel C.;Hunt, Harold W.;Hammel, Michal;Schulman, Brenda A.
通讯作者：
Schulman, Brenda A.
DOI：
10.1074/jbc.m112.352484
发表时间：
2012-08-24
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Emberley ED;Mosadeghi R;Deshaies RJ
通讯作者：
Deshaies RJ
DOI：
10.1016/j.biocel.2015.07.013
发表时间：
2015-09-01
影响因子：
4
作者：
Dubiel, Dawadschargal;Ordemann, Juergen;Naumann, Michael
通讯作者：
Naumann, Michael
影响因子：
64.5
作者：
Feldman, RMR;Correll, CC;Deshaies, RJ
通讯作者：
Deshaies, RJ