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. 2005 Jan 1;118(Pt 1):7-18.
doi: 10.1242/jcs.01620.

The molecular machinery of autophagy: unanswered questions

Daniel J Klionsky  1
Affiliations

The molecular machinery of autophagy: unanswered questions

Daniel J Klionsky. J Cell Sci. .

Abstract

Autophagy is a process in which cytosol and organelles are sequestered within double-membrane vesicles that deliver the contents to the lysosome/vacuole for degradation and recycling of the resulting macromolecules. It plays an important role in the cellular response to stress, is involved in various developmental pathways and functions in tumor suppression, resistance to pathogens and extension of lifespan. Conversely, autophagy may be associated with certain myopathies and neurodegenerative conditions. Substantial progress has been made in identifying the proteins required for autophagy and in understanding its molecular basis; however, many questions remain. For example, Tor is one of the key regulatory proteins at the induction step that controls the function of a complex including Atg1 kinase, but the target of Atg1 is not known. Although autophagy is generally considered to be nonspecific, there are specific types of autophagy that utilize receptor and adaptor proteins such as Atg11; however, the means by which Atg11 connects the cargo with the sequestering vesicle, the autophagosome, is not understood. Formation of the autophagosome is a complex process and neither the mechanism of vesicle formation nor the donor membrane origin is known. The final breakdown of the sequestered cargo relies on well-characterized lysosomal/vacuolar proteases; the roles of lipases, by contrast, have not been elucidated, and we do not know how the integrity of the lysosome/vacuole membrane is maintained during degradation.

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Figures

Fig. 1
Fig. 1
A schematic overview of autophagy and the Cvt pathway in yeast. The Cvt pathway is an autophagy-related process that operates under vegetative conditions and plays a biosynthetic role, delivering resident hydrolases such as aminopeptidase I (Ape1) to the yeast vacuole. The Cvt vesicle is approximately 150 nm in diameter and appears to exclude cytosol. In yeast, autophagy is induced by starvation, and the autophagosome, which is 300-900 nm in diameter, sequesters cytoplasm, including organelles; this pathway is also used for specific transport of prApe1. Both types of vesicle are thought to originate from the pre-autophagosomal structure (PAS). Upon completion, the vesicles fuse with the lysosome-like vacuole, releasing the inner vesicle, termed a Cvt body or autophagic body. These subvacuolar vesicles are broken down, allowing maturation of prApe1 and degradation of cytoplasm, with recycling of the resulting macromolecules.
Fig. 2
Fig. 2
Regulation of induction and vesicle nucleation. The regulation of autophagy has been characterized in studies of yeast and mammalian cells. (A) In yeast, a class III PI 3-K is required for autophagic activity and may function at the pre-autophagosomal membrane. A putative complex consisting of Atg1 kinase and several other proteins characterized as being required primarily for autophagy (in purple) or the Cvt pathway (in green) may be a downstream effector of Tor kinase to regulate the type of pathway that operates, depending on the nutritional conditions or other signals. Autophagy in yeast is primarily a starvation response; Tor, along with other regulatory components not shown (including PKA), responds to nutrient levels. In nutrient-rich conditions, Atg1 and Atg13 are more highly phosphorylated and have a lower affinity for each other; during starvation the two proteins are partially dephosphorylated. The PI 3-K complex I, consisting of Vps15, Vps34, Atg6/Vps30 and Atg14, is required for both the Cvt pathway and autophagy. (B) In mammalian cells, a class I PI 3-K is stimulated in response to the binding of a ligand to a receptor such as the insulin receptor (InR). PtdIns(3,4)P2 and PtdIns(3,4,5)P3 generated at the plasma membrane allow the binding and activation of 3-phosphoinositide-dependent protein kinase 1 (PDK1) and Akt/PKB, whereas PTEN antagonizes this pathway through its 3′-phosphoinositide phosphatase activity. Akt inhibits the GTPase-activating protein complex TSC1-TSC2, resulting in the stabilization of RhebGTP, which activates Tor, resulting in the inhibition of autophagy. Both Tor and PDK1 stimulate p70S6 kinase (p70S6k). The downregulation of p70S6k activity in starvation conditions (when Tor is inhibited) might prevent excessive autophagy (Scott et al., 2004). It is also possible that p70S6k indirectly inhibits Tor by interfering with activation of the class I PI 3-K, as suggested by studies in mammalian cells (Um et al., 2004). In nutrient-rich conditions, activation of p70S6k should inhibit PI 3-K, allowing a low level of autophagy for homeostatic purposes, whereas in starvation conditions the eventual inactivation of p70S6k should allow activation of PI 3-K to prevent excessive autophagy. The class III PI 3-K serves a stimulatory role possibly similar to that of the yeast enzyme complex.
Fig. 3
Fig. 3
Temporal order of action of cargo-packaging components. The yeast Cvt pathway is an example of specific autophagy. The resident vacuolar hydrolases Ape1 and Ams1 assemble into oligomers in the cytosol. Precursor (pr)Ape1 dodecamers further collect into a large Ape1 complex. The receptor/adaptor Atg19 binds to both the Ape1 complex (through the prApe1 propeptide) and Ams1. Atg11, a component that is not essential for autophagy, interacts with this Cvt complex and is required to connect the complex with the pre-autophagosomal structure (PAS). Atg11 also interacts with Atg1 (not shown, see Fig. 2A), but the timing of this interaction relative to cargo packaging is not known. Atg11 is not part of the final Cvt vesicle or autophagosome and presumably detaches from Atg19 at some time during or after the arrival of the Cvt complex at the PAS. Atg19 subsequently binds to Atg8-phosphatidylethanolamine, which is localized to the PAS, and this event might trigger completion of the vesicle.
Fig. 4
Fig. 4
Schematic model for formation of the autophagosome or Cvt vesicle. The origin of the membrane that forms the Cvt vesicle or autophagosome is not known, nor is the mechanism of vesicle formation. In one model (shown on the left), a membrane sheet from a pre-existing organelle such as the endoplasmic reticulum (ER) is induced to separate and undergo a deformation to form a spherical shape that eventually seals; no additional membrane is needed for expansion. It is not known when or how autophagy proteins such as Atg8 would be targeted to this membrane. In a second model (shown on the right), a portion of a membrane forms the nucleus of the autophagosome or Cvt vesicle; in yeast, this nucleus is the pre-autophagosomal structure (PAS). Additional membrane is added to allow expansion of the forming vesicle, but the origin of this membrane is not known. Most data support the second type of model. In either case, the original membrane is presumably equivalent on all surfaces in terms of protein content and phospholipid composition. During vesicle formation, the membrane may differentiate so that, upon vesicle completion, the two separate membranes have different properties; for example, Atg8-PE is located on both sides of the forming vesicle, but is removed from the outer membrane following cleavage by Atg4 (see Fig. 5). The outer vesicle membrane might contain SNARE elements needed for recognition and fusion with the vacuole (see Fig. 7), whereas the inner vesicle membrane might be more susceptible to degradation within the vacuole lumen. The double-membrane nature of the autophagosome or Cvt vesicle results in a transfer of the cargo from the cytosol into the lumenal space of the cell.
Fig. 5
Fig. 5
Vesicle expansion and completion. Two ubiquitin-like proteins participate in vesicle formation. The C-terminal arginine residue (R) of yeast Atg8 is removed by the Atg4 cysteine protease to reveal a glycine residue. Atg8 and Atg12 are ubiquitin-like proteins that are activated by the E1-like enzyme Atg7. Atg8 and Atg12 are then transferred to the E2-like enzymes Atg3 and Atg10 and are conjugated to phosphatidylethanolamine (PE) and Atg5, respectively. Atg8-PE becomes anchored in the membrane of the PAS and is a component of the forming and completed autophagosome or Cvt vesicle membrane. Atg12 and Atg5 bind Atg16 non-covalently and the self-interaction of Atg16 allows multimerization of the complex. A second cleavage by Atg4 releases Atg8 from the outer membrane of the completed vesicle. A similar set of reactions occurs in mammalian cells.
Fig. 6
Fig. 6
Protein retrieval from the PAS. Only two proteins are known to remain associated with completed yeast Cvt vesicles or autophagosomes, the specific receptor Atg19 and Atg8-PE; other proteins that are involved in vesicle formation presumably recycle from the PAS or the autophagosome/Cvt vesicle during formation. Most Atg proteins are soluble or peripheral membrane proteins that can easily be released from the membrane surface, although the mechanism of targeting and release is not known. As shown here, retrieval of Atg9 from the PAS requires PtdIns(3)P, the PtdIns(3)P-binding protein Atg18, and Atg2, Atg13 and Atg1.
Fig. 7
Fig. 7
Docking and fusion. Vam3, Vam7, Vti1 and Ykt6 are members of the SNARE family, proteins that function in membrane fusion in a variety of cellular contexts. Ypt7 is a member of the Rab small GTPase family, whose members are again implicated in many instances of membrane fusion. Also shown is the class C Vps/HOPS complex and two proteins recently shown to play a role in the fusion process, Ccz1 and Mon1.
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