AP‐3 vesicle uncoating occurs after HOPS‐dependent vacuole tethering

Heterotetrameric adapter (AP) complexes cooperate with the small GTPase Arf1 or lipids in cargo selection, vesicle formation, and budding at endomembranes in eukaryotic cells. While most AP complexes also require clathrin as the outer vesicle shell, formation of AP‐3‐coated vesicles involved in Golgi‐to‐vacuole transport in yeast has been postulated to depend on Vps41, a subunit of the vacuolar HOPS tethering complex. HOPS has also been identified as the tether of AP‐3 vesicles on vacuoles. To unravel this conundrum of a dual Vps41 function, we anchored Vps41 stably to the mitochondrial outer membrane. By monitoring AP‐3 recruitment, we now show that Vps41 can tether AP‐3 vesicles to mitochondria, yet AP‐3 vesicles can form in the absence of Vps41 or clathrin. By proximity labeling and mass spectrometry, we identify the Arf1 GTPase‐activating protein (GAP) Age2 at the AP‐3 coat and show that tethering, but not fusion at the vacuole can occur without complete uncoating. We conclude that AP‐3 vesicles retain their coat after budding and that their complete uncoating occurs only after tethering at the vacuole. Synopsis Vps41, part of the budding yeast homotypic fusion and vacuole protein sorting (HOPS) complex, has been implicated in formation of the AP‐3 vesicle coat, but also in fusion of AP‐3 vesicles with the vacuole. This study reveals that Vps41 is dispensable for the biogenesis of AP‐3 vesicles, but required for vacuolar tethering that can occur prior to complete vesicle uncoating. Vps41 anchored to the outer mitochondrial membrane can recruit AP‐3 vesicles. Generation of AP‐3 vesicle does not require Vps41 at the Golgi complex. The Arf1 GTPase‐activating protein (GAP) Age2 is present on AP‐3 vesicles. Age2 GAP function is required for AP‐3 vesicle transport to the vacuole. AP‐3 vesicles retain their coat until the tethering step at the vacuole. Graphical Abstract AP‐3 vesicles in budding yeast can form in the absence of the HOPS subunit Vps41, but require the HOPS complex for vacuolar tethering that can occur prior to complete vesicle uncoating.