Main

Under basal conditions, autophagy is dedicated to the continuous renovation of the intracellular pool of proteins, carbohydrates, lipids, and organelles, and thus plays a critical role in cellular homeostasis. Following external or internal stress, autophagy is rapidly upregulated and exerts a cytoprotective function. During this process, cellular materials or invaders are sequestered by double-membrane vesicles known as autophagosomes, and delivered to the lysosome for degradation1,2,3. Autophagy was initially described as a non-selective bulk process induced in response to starvation; however, it is now clear that the turnover of damaged organelles, removal of protein aggregates, and elimination of intracellular pathogens, are highly selective and tightly regulated processes that require cargo recognition by the autophagy machinery2,3,4,5. Several targets of selective autophagy have been described, such as aggregated proteins (aggrephagy), mitochondria (mitophagy), peroxisomes (pexophagy), ribosomes (ribophagy), endoplasmic reticulum (reticulophagy) and pathogens (xenophagy). Our knowledge about the network of autophagy regulators has increased dramatically, bringing a new understanding of this highly selective and precisely regulated membrane-dependent process. Following autophagy induction, the rapid formation of numerous autophagosomes relies on different membrane sources. Membranes are recruited and recognized by autophagy receptors, which participate in cargo sequestration and degradation. Importantly, the autophagy machinery is also employed by non-degradative cellular pathways such as the secretion of immuno-modulatory molecules and cytokines, endosome transport, and the activation of hydrolytic enzymes by the cytoplasm-to-vacuole targeting (Cvt) pathway in yeast6.

The core autophagosomal machinery

More than 30 autophagy-related (Atg) proteins have been identified in yeast7,8,9. Autophagy begins with the formation of a phagophore — a double-layered, crescent-shaped membrane — which expands to engulf cytoplasmic material, and then closes to form the autophagosome1 (Fig. 1a). Phagophore formation is primarily induced by the unc-51-like kinase (ULK1; Atg1 in yeast) complex, which can be regulated by the kinases AMPK (the cell energy sensor) and mTOR (the cell growth regulator)10,11,12,13,14. One of the crucial targets of ULK1 activity is the class III phosphatidylinositol 3-kinase (PI(3)K) complex, containing beclin 1 (Atg6 in yeast) and VPS34 (vacuolar protein sorting 34)15. When phosphorylated, beclin 1 promotes the local production of phosphatidylinositol 3-phosphate (PtdIns(3)P) by VPS34. PtdIns(3)P is recognized by early autophagic effector proteins that contain FYVE domains, such as Atg21 and WIPI1/2 (Atg18 in yeast)16,17. Although ULK1 is considered as the central autophagy regulator, there are ULK1-independent ways to trigger the autophagy cascade18,19. Moreover, ULK1-independent autophagy has been linked to non-canonical autophagic processes including LC3-associated phagocytosis (LAP; engulfment of extracellular particles in the form of cell debris or pathogens)20 and entosis (engulfment of a live epithelial cell by another epithelial cell)21.

Figure 1: Functions of autophagy receptors and adaptors in selective autophagy.
figure 1

(a) An LC3II-positive phagophore membrane forms around specific autophagic cargo based on the autophagy receptor. These receptors are characterized by their ability to simultaneously interact with autophagy modifiers (LC3/GABARAP/Atg8) and selective cargo, thus bridging the growing phagophore and targeted cargo. The phagophore then forms an intact, double-membrane autophagosome that encloses the cargo and subsequently fuses with the lysosome. Fusion allows for the lysosomal proteases to degrade the cargo together with its receptor and the inner autophagosomal membrane. (b,c) Several autophagy adaptors, that non-covalently bind autophagy modifiers, function in (b) autophagy initiation complex formation (ULK1, beclin 1, FIP200, VPS34) or in enzyme conjugation (ATG3, ATG7, ATG5, ATG12, ATG16) as well as in (c) fusion between autophagosomes and lysosome (SNX18) or microtubule transport machineries (FYCO1). The distinctive difference between autophagy receptors and autophagy adaptors is that adaptors are neither selective for cargos nor degraded within lysosomes with their respective cargos. Kinesin/dynein: motor proteins on the microtubule.

Full size image

The core autophagic machinery in yeast also includes two ubiquitin (Ub)-like proteins, Atg12 and Atg8. In contrast to many other Ub-like proteins, the C-terminal glycine residue of Atg8 is not conjugated to the lysine residue of another protein but to the amino group of phosphatidyl ethanolamine (PE). In mammals, the autophagic machinery increases in complexity and the relevant Atg8 homologues cluster in two subfamilies: MAP-LC3 (microtubule-associated protein light chain 3; referred to as LC3 hereafter) and GABARAPs/GATE-16 (reviewed in ref. 22). Both subfamilies are essential for autophagosome biogenesis and act at different steps of phagophore assembly23,24. Importantly, these modifiers of autophagosomal membranes are also critical factors in cargo sequestration during selective autophagy and vesicle trafficking.

Membrane sources and their potential role in selectivity

Formation of autophagosomes is a rapid process that mobilizes a large pool of intracellular membranes during engulfment of the substrate. In mammals, the endoplasmic reticulum (ER), the Golgi and mitochondria are suggested sources for phagophore initiation. In yeast, the formation of phagophores occurs at a defined place in close proximity to the vacuole, termed the pre-autophagosomal structure (PAS)25,26. The phagophore membrane is then further propagated through the fusion of vesicles originating from different membrane sources including the plasma membrane, the Golgi, recycling endosomes, and probably others (reviewed in refs 6,27). Despite intensive research, it is still unresolved how these different membrane sources feed into autophagosomal membranes, and whether they have distinct functions in autophagy pathways. Dependent on the stress source, selective autophagy may require the use of spatially restricted membrane pools, and thus the origin of the membrane might contribute to the selectivity of cargo recognition. Assuming an economic management of cellular resources, membrane-containing cargos such as depolarized mitochondria or pieces of ER destined for lysosomal destruction could donate membranes for growing phagophores. Although no evidence for such a scenario yet exists, a recent study on lipid droplets suggests that the activity of autophagy also depends on the local availability of lipids28.

Inter-organelle contact sites have emerged as dynamic spots for lipid transition between membranes and for the growth of nascent phagophores. Mitochondria-associated ER membranes (MAMs) are claimed to be the origin of phagophores in mammalian cells29,30. These organelles are the major sites of PE production31 and harbour key Atg proteins and their regulators. Moreover, microscopic and tomographic studies have provided direct evidence for the presence of initial stages of phagophore formation on these organelles29,32,33. Proteins responsible for tethering ER to mitochondria, mitofusin 2 (MFN2) and PACS-2, and ER resident protein syntaxin 17, are important for subsequent ATG5-dependent LC3 lipidation and the recruitment of early autophagy effectors, such as ATG14 (refs 29,30,34). MAMs spatially overlap with specialized membrane compartments called omegasomes (omega-shaped DFCP1-positive structures), which are supposed to originate from the ER and have been claimed to serve as a cradle of phagophore formation and autophagosomal vesicles close to the ER (ref. 35). PtdIns(3)P, the initial membrane mark for autophagosomal membranes, is abundant in omegasomes and recruits FYVE-domain containing effector proteins such as WIPI2 (yeast Atg18)36, which are required for the formation of LC3II-positive autophagosomes. All these findings strongly support that MAMs/omegasomes are an important initiation site for phagophores. How ER-associated omegasomes participate in the clearance of damaged mitochondria was recently visualized by microscopy37. This study unveiled that mitophagy occurs in a bit-by-bit manner at the intersection of parkin-labelled mitochondrial tubules and the ER (ref. 37). The ER also contacts the plasma membrane38 through tethering by extended synaptotagmins (E-Syts) via PtdIns(4,5)P2 interactions. These contact sites allow for crosstalk between the organelles independently of membrane trafficking (reviewed in ref. 39) and may, similarly to MAMs, serve as phagophore initiation sites under specific conditions.

Whereas a large body of evidence indicates that the ER and mitochondria might be the main source for phagophore initiation, components of the endocytic compartment can also contribute to the expansion of the autophagosome. Several key autophagic proteins such as ATG9, ULK1 or ATG16 as well as the PI(3)K complex localize to the different kinds of endosomes defined by present subsets of Rab GTPases. Furthermore, a recent study in mammalian cells demonstrated that the plasma membrane contributes to autophagosome biogenesis via two distinct routes: ATG9- and ATG16-positive vesicles. Vesicles generated in both pathways are LC3-negative and converge in the recycling endosome40. In yeast, a subfraction of Atg9-containing single-membrane vesicles fuse with autophagosomal membranes33,41. However, the majority of them only transiently associate with and recruit autophagic regulatory proteins — for example, Atg1, the TRAPPIII complex and Ypt1 — to the pre-autophagosomal membrane, rather than providing large amount of lipids42,43,44. Clearly, more molecular studies are needed to elucidate the entangled pathways that regulate membrane formation during different autophagy pathways.

Autophagy receptors are key players in selective autophagy

Whereas the autophagy response to starvation is bulk degradation of cytosolic material, other types of stresses such as damaged organelles or aggregated proteins require selective sequestration of the specific cargo into autophagosomal membranes. Selectivity is achieved through autophagy receptors, which recognize cargos tagged with degradation signals and the autophagosomal membrane through their LC3-interacting regions (LIR). LIR motifs in general interact with autophagy modifier proteins of the LC3/GABARAP family22. In yeast, five receptors have been described so far to mediate cargo selection: Atg19 and Atg34 (Cvt pathway), Atg32 (mitophagy), Atg36 (pexophagy), and Atg30 (pexophagy), several of which have homologues in higher eukaryotes9. In mammalian cells, more than two dozen autophagy receptors were identified by the yeast two-hybrid system and proteomic approaches45,46. Not all proteins interacting with Atg8, LC3s or GABARAPs are autophagy receptors. An autophagy receptor is defined by its ability to bridge cargo and autophagosomal membrane, leading to the engulfment of cargo by the autophagic membrane (Fig. 2a). There is an additional class of proteins — autophagy adaptors — that also bind to members of the Atg8 family. However, they do not facilitate engulfment and subsequent degradation of cargo, but serve as anchor points for the autophagy machinery and regulate initiation, conjugation, transport and fusion of autophagosomes (Fig. 1b,c).

Figure 2: The selective recruitment of phagophores to cargos through the interaction of autophagy receptors with LC3II in different selective autophagy pathways.
figure 2

(a) In mitophagy, p62 recognizes poly-ubiquitylated (Ubn, purple) mitochondria destined for autophagosome degradation. Alternatively, mitochondria can also be bound by NIX directly without necessitating poly-ubiquitylation. In aggrephagy, poly-ubiquitylated protein aggregates are engulfed by the phagophore via p62 and NBR1. In xenophagy, the autophagic receptor proteins NDP52, p62 and OPTN recognize poly-ubiquitylated bacteria. In this case, the association of the LIR motif with LC3II can be enhanced by TBK1-dependent OPTN phosphorylation. Lastly, for pexophagy, p62 and NBR1 recruits the LC3II-positive phagophore to mono-ubiquitylated peroxisomes. (b) Domain structure of autophagy receptors involved in selective autophagy pathways, containing distinct ubiquitin-binding domains (blue) and LC3-interacting motifs (LIR, red).

Full size image

The most prevalent autophagy targeting signal in mammals is the modification of cargos with Ub (ref. 4). The efficiency of ubiquitylation as a cargo signal was shown by ubiquitylation of endogenous proteins on the surface of mitochondria or pathogens such as Salmonella enterica, and by the artificial attachment of monoubiquitin to the cytosolic side of peroxisomes or long-lived cytosolic proteins47, which is both required and sufficient to induce their autophagic clearance. Indeed, most of the currently known autophagy receptors harbour both Ub-binding domains (UBDs) and LIRs (ref. 48) (Fig. 2b). On the other hand, selective autophagy in yeast does not use Ub modifications as a degradation signal, similarly to the mammalian autophagy receptors NIX or BNIP3, which are located at the outer mitochondrial membrane (reviewed in ref. 49; see below).

In higher organisms, autophagy receptors and mechanisms involved in mitophagy are probably the best studied so far. Depolarization of mitochondria leads to activation of PINK1 (PTEN-induced putative kinase protein 1) that accumulates at the outer mitochondrial membrane and phosphorylates numerous proteins50. Subsequent recruitment of the E3 ligase Parkin leads to multiple poly-Ub proteins51,52,53,54,55, which are recognized and clustered through polymerization by the autophagy receptor p62/SQSTM1 (sequestosome-1)56. Unexpectedly, p62 localizes to the phagophore even in the absence of LC3 interaction57. There is some evidence that self-oligomerization of p62 via the PB1 domain rather than binding to LC3 is critical for the translocation of p62 to the autophagosomal membrane57. Whereas the autophagic degradation of p62 loaded with selective cargo is dependent on the LIR–LC3 interaction, the initial targeting of p62 to autophagosomal membranes might not require the LIR domain.

These mechanisms for mitophagy have mostly been discovered under rather artificial conditions such as the treatment of cells with the mitochondrial uncoupling reagent CCCP and overexpression of Parkin, and so it has been questioned whether they take place in a physiological context. Whereas p62 is required for Parkin-mediated mitochondrial clustering as described, it may not be essential for efficient mitophagy under certain conditions56. In addition, the Ub ligase Parkin is dispensable for the clearance of dysfunctional mitochondria in mice58, indicating the presence of redundant, Ub-independent mitophagy pathways and/or additional autophagy receptors playing a redundant role for p62-mediated mitophagy56. In fact, during erythrocyte differentiation or in response to hypoxia, the removal of mitochondria can be mediated by NIX, BNIP3 and FUNDC1 (refs 59,60,61). All three receptors are mitochondrial outer-membrane proteins that can directly link mitochondria to autophagosomal membranes via their LIR domain in a Ub-independent way. Two reports hypothesize a regulatory function of these receptors: BNIP3 and NIX can trigger mitochondrial depolarization62 and NIX might also promote the mitochondrial translocation of Parkin, thereby contributing to Parkin–Ub–p62-mediated mitochondrial priming63. In addition, NIX regulates undamaged mitochondria in response to their energetic activity: high oxidative phosphorylation activity leads to the accumulation of the small GTPase Rheb on the mitochondrial outer membrane, where it physically interacts with NIX and enhances the autophagic removal of the undamaged organelle64.

An autophagy-receptor-independent mechanism of mitophagy was recently discovered in neuronal cells, and involves the inner mitochondrial membrane phospholipid cardiolipin. Mitophagy-stimulating substances caused cardiolipin externalization to the outer mitochondrial membrane, where it was directly recognized by LC3 (ref. 65) and facilitated mitophagy. In yeast, the removal of damaged mitochondria via autophagy generally happens independently of Ub. Comparable to NIX, the mitochondrial-anchored receptor Atg32 links damaged mitochondria to autophagosomal membranes66. It might be that Ub-independent selective autophagy pathways developed first, and then Ub-dependent pathways were developed by higher eukaryotes to speed up the autophagic process and introduce additional regulatory layers, such as recruitment of the Ub ligase Parkin by NIX (ref. 63) and phosphorylation of p62 and optineurin (OPTN), leading to increased Ub- and LC3-binding affinities, respectively67,68,69 (see below).

Another intriguing feature of autophagy receptors is their tendency to oligomerize, which further facilitates sequestration and clustering of the autophagic cargo. This formation of larger aggregates or inclusions (also called 'sequestosomes') could constitute a crucial step towards degradation by autophagy, as has been observed during the removal of defective mitochondria in mammals via p62 (refs 56,57) and during aggrephagy in mammalian cells45 and Drosophila brain70. Impairment in aggrephagy leads to formation of inclusion bodies containing poly-Ub protein aggregates that are hallmarks of neurodegenerative diseases such as Parkinson's or Alzheimer's disease. Genetic inactivation of p62 in mice or Ref(2)P (the Drosophila homologue of p62) in Drosophila models of neurodegenerative diseases revealed that p62 plays an important role in the formation of these inclusion bodies70,71 and contributes to their autolysosomal elimination72.

Selective autophagy receptors lack a clear specialization but often cooperate with each other in selecting a specific cargo: the autophagic receptor NBR1 (neighbour of BRCA1) interacts with p62 and plays an essential role in p62-dependent sequestration and degradation of aggregated proteins45, peroxisomes73, and mid body rings74. On the other hand, during xenophagy, p62 teams up with OPTN and NDP52 (refs 67,75,76) to facilitate the removal of invading bacteria. All of the receptors seem to have certain specificities, as they are recruited independently, and depletion of only one of them impairs bacterial clearance77. Notably, NDP52 is able to recognize invading bacteria not only through binding to Ub but also through binding to cytosolic lectin galectin-8 (ref. 75).

Little is known about the mechanisms governing selectivity in ribophagy and reticulophagy. Yeast ribophagy is dependent on the Ubp3/Bre5 deubiquitylation complex78 that also regulates the Cvt pathway through its action on Atg19 (ref. 79). Recent work indicates that there is an interplay between the Ubp3/Bre5 deubiquitylation and the E3 ligase Ltn1 in the regulation of ribophagy80.

We are only beginning to understand how cargos for selective autophagy are recognized and how this process is regulated. Further specific degradation signals and novel receptors are expected to be unveiled, such as the adaptor protein AP2 that was recently identified as a cargo receptor for aggregation-prone proteins involved in Alzheimer's disease81. Other examples of newly discovered regulators of autophagy are the proto-oncogene c-Cbl, which targets active Src in cancer cells via a newly identified LC3-interacting region to autophagosomes82, and cardiolipin, the only lipid-based autophagy linker between cargo and autophagosomes identified so far65.

Regulation of autophagy receptors

The activity of autophagy receptors is tightly regulated by inducible expression, spatial organization and cellular localization, and multiple post-translational modifications. To maintain a low basic protein level without accumulation in times of low autophagy, most receptors and scaffold proteins undergo constant degradation by autophagy even in an unloaded state.

More specific regulation occurs by post-translational modifications. As mentioned, selective autophagy in yeast does not use ubiquitylation to initiate degradation and therefore putative cargos need protection from constant undesired removal. In yeast, the known five receptors involved in cargo selection are localized in an inactive form on the cargo organelle and, following autophagy induction, interact with Atg8 and the basic autophagic scaffold Atg11 in a phosphorylation-dependent manner66,83,84. Atg11 can bind to cargo receptors as well as to components of the autophagy machinery. Thus the recruitment of cargo into autophagosomes not only depends on Atg8 but on a tripartite interaction of the receptor–cargo complex with the autophagosomal membrane (via Atg8) and core components of the autophagosomal machinery (via the scaffold Atg11). Both interactions are controlled by phosphorylation of the Atg11 and Atg8 binding sites of autophagy receptors by as-yet unknown kinases85. Studies in higher eukaryotes also identified scaffold proteins involved in specific types of autophagy, such as mammalian ALFY (ref. 86) and EPG-7 in C. elegans87. Moreover, phosphorylation as an inducing event of autophagy is conserved from yeast to mammals: phosphorylation of the LIR domain of BNIP3 activates its interaction with LC3s (ref. 88), and specific phosphorylation of the autophagy receptors p62 and OPTN results in increased affinity to Ub chains and LC3, shown to be essential for autophagic clearance of cytosolic salmonella67,68,69,89. It will be a challenge to identify the multiple post-translational modifications that govern autophagy selectivity and spatiotemporal regulation.

Secretory pathways use the autophagy machinery

Processes involving molecules and mechanisms of the autophagic machinery in controlling secretory pathways have been recently identified. Such autophagy-dependent secretion allows the cell to secret proteins that lack a conventional secretory signal sequence. In yeast this is implicated by the formation of a 'compartment for unconventional protein secretion' (CUPS). Initiation of CUPS seems to occur independently of the PAS and autophagosomes dedicated for the Cvt pathway, but CUPS shares several features with omegasomes in mammalian cells: CUPS is enriched in PtdIns(3)P and Atg8, and forms close to the ER (ref. 90). Besides the involvement of specific Atg factors, CUPS is characterized by the dependence on Golgi re-assembly and stacking proteins (GRASPs). Illustrating the interdependency of membrane trafficking and unconventional autophagosomal pathways, IL-1β secretion in mammalian cells is inhibited during basal autophagy91,92 and upregulated following autophagy induction93. Additionally, the autophagosome contributes effector molecules (hydrolases) for the correct processing of IL-1 family members. The role of selective autophagy during the secretion of effector molecules can also be observed in osteoclasts (Fig. 3a). In these specialized cells, secretory lysosomes fuse with the plasma membrane juxtaposed to bone to create the ruffled border, a cellular organelle responsible for resorbing the osseous tissue in osteoclasts. The formation of the ruffled border relies on several autophagic proteins including ATG5, ATG7, ATG4B and LC3 (ref. 94).

Figure 3: Selective autophagy regulates secretion and transport processes.
figure 3

(a) Formation of the ruffled border in osteoclasts and secretion of lysosomal proteins lead to resorption of bone tissue. In this process, cathepsin-K-containing lysosomes are recruited to and subsequently fuse with the plasma membrane in an LC3II-dependent manner. (b) The formation of a LC3II-positive single-layer membrane around bacteria or dead cells results in phagocytosis. Subsequent fusion with a lysosome forms the phagolysosome, where the cargo is then degraded.

Full size image

Autophagy-dependent secretion has also been implicated in the pathology of Crohn's disease, a polygenic inflammatory disease involving the small intestine. Mutations in several autophagy-related genes, including ATG16L1 and NOD2, are associated with Crohn's disease. NOD2 is a pattern-recognition-receptor (PRR) that senses invading pathogens and induces their autophagic elimination at the plasma membrane95 (Fig. 3b). Moreover, ATG16L1 as well as ATG5 and ATG7 are crucial for the secretion of granule contents of the Paneth cell, a specialized secretory epithelial cell96. It remains unclear how the interplay between the secretory system and autophagy machinery affects the final fate of the transport cargo — particularly in terms of what determines the fusion events between different intracellular membranes along these pathways, and what mechanisms engage the autophagy components in secretion pathways rather than promoting cargo transport to the lysosome for degradation.

Overlapping roles of autophagy and intracellular trafficking

Autophagy shares many central features with membrane trafficking pathways, including membrane remodelling, the budding of vesicles, their directed movement along microtubule tracks, and the homo- as well as heterotypic fusion of vesicles6. As both types of transport systems rely on the same functional modules, membrane trafficking pathways can be regulated by autophagy and, vice versa, several proteins controlling intracellular transport can modulate autophagy.

A family of important regulators of endocytic trafficking are the RabGAPs, which control the GTPase activity of Rab proteins (reviewed in ref. 97). Several RabGAPs have been recently reported to play an important role in autophagy — such as TBC1D14, which mediates autophagosome growth by regulating Rab11 and recycling endosomes, and interacting at the same time with ULK1 and TBC1D25, which mediates fusion of autophagosome and lysosomes98,99. In addition, TBC1D5 regulates both retrograde transport (from endosomes to the trans-Golgi network, TGN) and autophagy flux100,101. The late-endosome marker TBC1D15, which is necessary for the recruitment of the tethering complex HOPS, associates with mitochondria via the fission protein Fis1 and contributes to their selective removal by autophagy102. In addition, the transport between the Golgi complex and ER depends on coatomer subunits α-, β- and ε-COP (refs. 103,104,105), which are at the same time critical for autophagy, as depletion of β′-, β- or α-COP results in an accumulation of autophagosomes and amphisomes106.

On the other hand, mammalian Atg8 family members are implicated in the regulation of the membrane fusion machinery107, which mediates the recognition and fusion of a transport vesicle and its target membrane independently of autophagy. Soluble (not lipidated) GATE-16 was shown to modulate intra-Golgi transport as well as post-mitotic Golgi re-assembly by coupling N-ethylmaleimide-sensitive factor (NSF) activity and SNAREs activation, and by regulating NSF function108,109. GATE-16 preferentially binds the unpaired form of a mitochondrial v-SNARE and interferes with the binding to its cognate t-SNARE (refs 109,110), thus preventing the assembly of SNARE complexes at inappropriate times109. Also, an interaction of GABARAP with NSF is required for the ability of GABARAP to regulate trafficking of the GABAA receptor, the predominant inhibitory neurotransmitter receptor in the brain111,112.

Finally, selective autophagy and the endolysosomal sorting of plasma membrane proteins employ the same strategy of cargo delivery. Both systems use Ub as a degradation signal and Ub-binding proteins as specific receptors that link cargo destined for lysosomal degradation. The plasma membrane can also directly contribute to the autophagy pathway by promoting internalization and trafficking of ATG9- and ATG16L1-positive vesicles needed for autophagosome formation40,100. The mechanisms governing endocytosis and lysosomal sorting have been extensively studied, and more principles that also apply to selective autophagy might be unravelled in the future.

Concluding remarks and future directions

The plethora of processes regulated by selective autophagy is indicative of its unique importance for cellular homeostasis in health and disease. Selective autophagy clearly goes beyond a simple 'eating' process involving double membranes, as it also directly or indirectly controls secretion and other intracellular transport processes. Apparently, lipid-conjugated Ub-like modifiers such as Atg8 in yeast and LC3/GABARAPs in mammals provide a regulatory network that combines the characteristics of the Ub system with the specialized functions of cellular membranes, making it an extremely versatile and generally applicable regulatory process. We have just begun to understand the molecular basis of how these adaptive networks cooperate to achieve the tremendous diversity observed in cells. Although several key findings have unravelled the basic principles of autophagosome formation and cargo selection by autophagic receptors, many questions remain. These are related to the molecular events that govern the very early steps of selective autophagy induction, the source of autophagic membranes, and their interplay with other endosomal membranous systems. Selective autophagy pathways can also positively and negatively impact human disorders including inflammation, infectious and neurodegenerative diseases, and cancer. Consequently, this evidence has attracted increased attention from the pharmaceutical industry for the development of the next generation of drugs.