The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway

Abstract

The transport protein particle (TRAPP) III complex, comprising the TRAPPI complex and additional subunit Trs85, is an autophagyspecific guanine nucleotide exchange factor for the Rab GTPase Ypt1 that is recruited to the phagophore assembly site when macroautophagy is induced. We present the single-particle electron microscopy structure of TRAPPIII, which reveals that the domeshaped Trs85 subunit associates primarily with the Trs20 subunit of TRAPPI. We further demonstrate that TRAPPIII binds the coat protein complex (COP) II coat subunit Sec23. The COPII coat facilitates the budding and targeting of ER-derived vesicles with their acceptor compartment. We provide evidence that COPII-coated vesicles and the ER-Golgi fusion machinery are needed for macroautophagy. Our results imply that TRAPPIII binds to COPII vesicles at the phagophore assembly site and that COPII vesicles may provide one of the membrane sources used in autophagosome formation. These events are conserved in yeast to mammals.M acroautophagy is a highly conserved catabolic process that uses a specialized membrane trafficking pathway to target proteins and organelles for degradation (1). Defects in this process have been linked to a variety of human diseases, including neurodegenerative diseases such as Parkinson's disease (2). Macroautophagy is induced by a variety of physiological stresses and begins with the expansion of a cup-shaped nucleating membrane called the phagophore, or isolation membrane. As the phagophore expands, it engulfs intracellular proteins and membranes that are marked for degradation. This expanding membrane eventually closes to become an autophagosome, a double-membrane structure that seals its contents from the cytosol and delivers it to the lysosome or vacuole for degradation. A central unanswered question in the autophagy field is the mechanism by which the phagophore forms and matures into an autophagosome. Although it was once thought that the phagophore assembles de novo, recent evidence suggests it forms from a preexisting compartment. Compartments on the secretory pathway, including the endoplasmatic reticulum (ER) and Golgi complex, have been invoked in phagophore assembly (3, 4).A collection of ATG (autophagy-related) genes, the products of which regulate autophagy, were identified in the yeast Saccharomyces cerevisiae (1). Many of the Atg proteins needed for macroautophagy in yeast are shared with the biosynthetic cytoplasm to vacuole targeting (Cvt) pathway that transports certain hydrolases into the vacuole. Both pathways require the sequestration of cargo within a double-membrane structure; however, only the macroautophagy pathway is conserved in higher eukaryotes (5). When autophagy is induced, ATG gene products assemble at the phagophore assembly site (PAS) in a hierarchical manner. The scaffold protein complex that organizes this site is the Atg17 complex (6, 7).Previous studies have shown that the transport protein particle (TRAPP) III complex, an autophagy-specic guanine nucleotide exchange factor (GEF) for ...

Membrane dynamics in autophagosome biogenesis

“…Moreover, the conserved oligomeric Golgi (COG) complex, another Ypt1 effector, localizes to the PAS and is required for proper localization of Atg8 and Atg9 (Yen et al, 2010). Interestingly, the TRAPPIII complex interacts with a subunit of the coat protein complex (COP)II, suggesting that COPII vesicles might provide membrane for phagophore formation and/or elongation (Tan et al, 2013). It is not known whether TRAPP complexes are involved in autophagy in mammalian cells, but as RAB1 and functional ER exit sites (ERES) have been implicated in autophagosome biogenesis (Graef et al, 2013;Zoppino et al, 2010) it is likely that ERES-derived COPII-coated vesicles also provide membrane to the growing phagophore in a TRAPP-dependent manner.…”

Managing the Adaptive Proteostatic Landscape: Restoring Resilience in Alpha-1 Antitrypsin Deficiency

“…Class I and II HDAC activity is reduced in the lung of COPD patients even though the HAT activity remains unchanged [ 265 , 266 ]. Moreover, reduction of HDAC2 causes corticosteroid resistance in COPD patients [ 267 ] leading to defective regeneration of airway epithelium [ 221 ], and reduction of HDAC3 increases the cytokine expression which would enhance infl ammatory responses [ 268 ]. Besi des the members of Class I and II, Zn 2+ -dependent HDACs targeted by SAHA, SIRT1, one of the class III NAD (+)-dependent HDACs, is also reduced in lung of COPD patient [ 269 ].…”

Preparing the Membrane for Autophagosome Biogenesis

“…These studies indicate a physiological and functional link between the COPII-enriched spot, the ERES (a functional equivalent of both the ERGIC and ERES of mammalian cells) and the PAS in yeast. As another support of this notion, depletion of COPII components has been shown to compromise autophagy in both yeast and mammalian cells [44,45,[48][49][50].…”

“…It is still unknown how bulk amount of ER membrane is directly mobilized for phagophore growth. COPII vesicle involvement could be one way [44,50,61]. However, other mechanisms may also exist.…”

“…The TRAPPIII complex associates withSec23, an integral component of COPII, and is a GTP Exchange Factor (GEF) of a small GTPase Ypt1 in yeast. Therefore COPII vesicles and Ypt1 are recruited to the PAS, where COPII vesicles supply membrane and Ypt1 regulates vesicular events [50,[74][75][76]. Furthermore, it is proposed that the TRAPPIII complex may also be a tether to facilitate heterotypic fusion between an Atg9 vesicle and a COPII vesicle in the PAS [50,77].…”