The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions, ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis, where a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodelling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of the ER and the role of individual ER-phagy receptors is limited. Here we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodelling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodelling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both the magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodelling and versatile genetic toolkit provide a quantitative framework for understanding the contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.

内质网 (ER) 利用多样化的蛋白质组景观来协调许多细胞功能，从蛋白质和脂质合成到钙离子流动和细胞器间通讯。一个恰当的例子涉及神经发生的过程，其中精细的管状内质网网络通过内质网成形蛋白组装成新形成的神经元投射，以创建高度极化的树突和轴突。先前的研究表明自噬在 ER 重塑中发挥作用，因为体内自噬缺陷的神经元在突触纽带内表现出轴突 ER 积累，并且膜嵌入的 ER 吞噬受体 FAM134B 与人类感觉和自主神经病变有遗传联系。然而，我们对选择性去除 ER 的机制以及单个 ER 吞噬受体的作用的理解是有限的。在这里，我们将用于监测体外分化过程中内质网重塑的遗传易处理诱导神经元（iNeuron）系统与蛋白质组和计算工具结合起来，通过选择性自噬创建内质网蛋白质组重塑的定量图谱。通过对单一和组合 ER 吞噬受体突变体的分析，我们描述了每种受体对 ER 蛋白清除的程度和选择性的贡献程度。我们将内质网膜或腔蛋白的特定子集定义为不同受体的首选客户。使用空间传感器和通量报告器，我们展示了轴突中 ER 的受体特异性自噬捕获，并通过冷冻电子断层扫描直接可视化神经元投影中自噬体内的管状 ER 膜。内质网蛋白质组重塑的分子库存和多功能遗传工具包为理解个体内质网吞噬受体在细胞状态转变过程中重塑内质网的贡献提供了一个定量框架。