Regulation of selective autophagy onset by a Ypt/Rab GTPase module

Abstract

The key regulators of intracellular trafficking, Ypt/Rab GTPases, are stimulated by specific upstream activators and, when activated, recruit specific downstream effectors to mediate membrane-transport events. The yeast Ypt1 and its human functional homolog hRab1 regulate both endoplasmic reticulum (ER)-to-Golgi transport and autophagy. However, it is not clear whether the mechanism by which these GTPases regulate autophagy depends on their well-documented function in ER-to-Golgi transport. Here, we identify Atg11, the preautophagosomal structure (PAS) organizer, as a downstream effector of Ypt1 and show that the Ypt1-Atg11 interaction is required for PAS assembly under normal growth conditions. Moreover, we show that Ypt1 and Atg11 colocalize with Trs85, a Ypt1 activator subunit, and together they regulate selective autophagy. Finally, we show that Ypt1 and Trs85 interact on Atg9-containing membranes, which serve as a source for the membrane component of the PAS. Together our results define a Ypt/Rab module-comprising an activator, GTPase, and effector-that orchestrates the onset of selective autophagy, a process vital for cell homeostasis. Furthermore, because Atg11 does not play a role in ER-to-Golgi transport, we demonstrate here that Ypt/Rabs can regulate two independent membrane-transport processes by recruiting process-specific effectors.

Autophagic Processes in Yeast: Mechanism, Machinery and Regulation

“…Another possibility is that the Atg9-positive vesicles assemble in a SNARE-dependent process (Nair et al 2011) to generate larger structures corresponding to the peripheral sites and at least one of these structures relocates near the vacuole surface to become the PAS (Mari et al 2010). Nevertheless, Atg9-positive membranes are probably maturing into the PAS/phagophores possibly by fusing together or with other membranes, as suggested by the colocalization of Atg9 with Ypt1 and the TRAPPIII complex (Lynch-Day et al 2010;Lipatova et al 2012) and the recruitment of these latter factors onto autophagosomal membranes by Atg9 .…”

Atg11

“…Atg11 interacts directly via its coiled-coil domains with both Atg9 and Atg19 as well as the PAS-localized Atg1, which allows it to bring Atg9-containing membrane and Atg19-prApe1 oligomers to the PAS. 10 What Lipatova et al 7 now show is that Atg11 also interacts with Ypt1 in a GTP-dependent manner, and as such appears to function as a classical Rab effector membrane tether. They first demonstrate this interaction with a yeast two-hybrid assay, and map the interacting region to coiled-coil domains 2 and 3 (CC2-3) of Atg11.…”

“…1). 5,6 Now, in a recent paper, Lipatova et al 7 define a new coiled-coil tether, Atg11, which acts as an effector of the Rab Ypt1 and the TRAPPIII complex during selective macroautophagy (see the punctum by Lipatova and Segev in this issue).…”

Structural biology of the macroautophagy machinery

“…Because Atg9 vesicles likely contribute only a small amount of membranes to autophagosomes, these specialized lipid vesicles may possess alternative functions. Indeed, recent studies revealed that Atg9 recruits the TRAPPIII vesicle tethering complex and Ypt1 Rab GTPase to the PAS Lipatova et al, 2012).…”