Autophagosome Biogenesis in Primary Neurons Follows an Ordered and Spatially Regulated Pathway

Autophagy is an essential degradative pathway in neurons, yet little is known about mechanisms driving autophagy in highly polarized cells. Here, we use dual-color live-cell imaging to investigate the neuron-specific mechanisms of constitutive autophagosome biogenesis in primary dorsal root ganglion (DRG) and hippocampal cultures. Under basal conditions, autophagosomes are continuously generated in the axon tip. There is an ordered assembly of proteins recruited with stereotypical kinetics onto the developing autophagosome. Plasma- or mitochondrial-derived membranes were not incorporated into nascent autophagosomes in the distal axon. Rather, autophagosomes are generated at double FYVE-containing protein 1 (DFCP1)-positive subdomains of the endoplasmic reticulum (ER), distinct from ER exit sites. Biogenesis events are enriched distally; autophagosomes form infrequently in dendrites, the soma, or midaxon, consistent with a compartmentalized pathway for constitutive autophagy in primary neurons. Distal biogenesis may facilitate degradation of damaged mitochondria and long-lived cytoplasmic proteins reaching the axon tip via slow axonal transport. •Autophagosomes in primary neurons form via an ordered assembly pathway•Neuronal autophagosomes form at DFCP1-positive subdomains of the ER•Autophagosome biogenesis in primary neurons is enriched in the distal axon•Constitutive autophagy follows a compartmentalized pathway in primary neurons Autophagy is a degradation pathway critical for neuronal viability. Maday and Holzbaur define the mechanisms of autophagosome biogenesis in primary neurons. Autophagosomes form via an ordered recruitment of proteins onto the ER. This process is enriched in the distal axon, indicating a compartmentalized pathway for constitutive autophagy in primary neurons.