The nuclear envelope (NE) is structurally and functionally vital for eukaryotic cells, yet its protein constituents and their functions are poorly understood in plants. Here, we combined subtractive proteomics and proximity-labelling technology coupled with quantitative mass spectrometry to understand the landscape of NE membrane proteins in Arabidopsis. We identified ~200 potential candidates for plant NE transmembrane (PNET) proteins, which unravelled the compositional diversity and uniqueness of the plant NE. One of the candidates, named PNET1, is a homologue of human TMEM209, a critical driver for lung cancer. A functional investigation revealed that PNET1 is a bona fide nucleoporin in plants. It displays both physical and genetic interactions with the nuclear pore complex (NPC) and is essential for embryo development and reproduction in different NPC contexts. Our study substantially enlarges the plant NE proteome and sheds new light on the membrane composition and function of the NPC.

核被膜 (NE) 在结构和功能上对真核细胞至关重要，但其蛋白质成分及其功能在植物中却知之甚少。在这里，我们将减法蛋白质组学和邻近标记技术与定量质谱相结合，以了解拟南芥中 NE 膜蛋白的景观. 我们确定了约 200 种植物 NE 跨膜 (PNET) 蛋白的潜在候选物，揭示了植物 NE 的组成多样性和独特性。其中一个名为 PNET1 的候选者是人类 TMEM209 的同源物，而 TMEM209 是肺癌的关键驱动因素。一项功能研究表明，PNET1 是植物中真正的核孔蛋白。它显示与核孔复合体 (NPC) 的物理和遗传相互作用，对于不同 NPC 环境中的胚胎发育和繁殖至关重要。我们的研究大大扩大了植物 NE 蛋白质组，并为 NPC 的膜组成和功能提供了新的线索。