Deubiquitinating enzymes and the proteasome regulate unique sets of ubiquitin substrates.

The ubiquitin-proteasome axis has been extensively explored at a system-wide level, but the impact of deubiquitinating enzymes (DUBs) on the ubiquitinome remains largely unknown. Using UbiSite technology and inhibitors, we have compared the contributions of the proteasome and DUBs on the ubiquitinome. We uncovered large differential dynamic Ub signalling networks with substrates and sites uniquely regulated by DUBs or by the proteasome, highlighting the role of DUBs in degradation-independent ubiquitin signalling. DUBs regulate substrates via nearly 40,000 unique sites. Moreover, we found that ubiquitin conjugated to SUMO2/3 forms a unidirectional proteasomal degradation signal with strikingly rapid kinetics compared to ubiquitin polymers only. We found that PARP1, is hyper ubiquitinated in response to DUB inhibition, increasing its enzymatic activity. Our findings highlight the key regulatory roles of DUBs on ubiquitin dynamics.

泛素-蛋白酶体轴（ubiquitin-proteasome axis）已在系统层面得到广泛研究，但去泛素化酶（deubiquitinating enzymes, DUBs）对泛素组（ubiquitinome）的影响仍在很大程度上未被探明。本研究借助UbiSite技术（UbiSite technology）与抑制剂，对比了蛋白酶体与去泛素化酶对泛素组的调控贡献。我们揭示了大量具有显著差异的动态泛素（Ub）信号网络，其底物与修饰位点分别由去泛素化酶或蛋白酶体进行独有调控，凸显了去泛素化酶在不依赖降解的泛素信号通路中的作用。去泛素化酶通过近4万个独特的修饰位点对底物实施调控。此外，我们发现与小泛素相关修饰物2/3（SUMO2/3）结合的泛素，可形成一种单向蛋白酶体降解信号，其动力学特性相较于仅由泛素聚合物（ubiquitin polymers）构成的信号而言极为迅速。我们发现，多聚ADP核糖聚合酶1（PARP1）在去泛素化酶抑制作用下会发生过度泛素化，进而提升其酶促活性。本研究结果凸显了去泛素化酶在泛素动态调控中的关键作用。