The inner nuclear membrane (INM) selectively accumulates proteins that are essential for nuclear functions; however, overaccumulation of INM proteins results in a range of rare genetic disorders. So far, little is known about how defective, mislocalized, or abnormally accumulated membrane proteins are actively removed from the INM, especially in plants and animals. Here, via analysis of a proximity-labeling proteomic profile of INM-associated proteins in Arabidopsis, we identify critical components for an INM protein degradation pathway. We show that this pathway relies on the CDC48 complex for INM protein extraction and 26S proteasome for subsequent protein degradation. Moreover, we show that CDC48 at the INM may be regulated by a subgroup of PUX proteins, which determine the substrate specificity or affect the ATPase activity of CDC48. These PUX proteins specifically associate with the nucleoskeleton underneath the INM and physically interact with CDC48 proteins to negatively regulate INM protein degradation in plants.

内核膜（INM）选择性地积累核功能所必需的蛋白质；然而，INM 蛋白的过度积累会导致一系列罕见的遗传性疾病。到目前为止，人们对有缺陷的、错误定位的或异常积累的膜蛋白是如何从 INM 中主动清除的知之甚少，尤其是在植物和动物中。在这里，通过分析拟南芥中 INM 相关蛋白的邻近标记蛋白质组图谱，我们确定了 INM 蛋白降解途径的关键成分。我们表明，该途径依赖于 CDC48 复合物进行 INM 蛋白提取，并依赖 26S 蛋白酶体进行后续蛋白降解。此外，我们发现 INM 处的 CDC48 可能受到 PUX 蛋白亚组的调节，这些蛋白亚组决定底物特异性或影响 CDC48 的 ATP 酶活性。这些 PUX 蛋白与 INM 下方的核骨架特异性结合，并与 CDC48 蛋白发生物理相互作用，从而负向调节植物中 INM 蛋白的降解。