Autophagy in Nonmammalian Systems

Abstract

Autophagy, or ‘self‐eating’, is a catabolic process that enables lysosome‐mediated degradation of cytoplasmic contents and recycling of macromolecules to be used in essential cellular processes. This process enables cells to survive during nutrient restriction, participates in cell death during development and functions in clearance of protein aggregates and intracellular pathogens. Autophagy has been widely studied in yeast, Drosophila and Caenorhabditis elegans, and studies in these organisms have revealed regulation by multiple cellular pathways. These include cell growth regulators, such as the Class I PI3 kinase and target of rapamycin (Tor), as well as cell death regulators, including caspases. Defects in autophagy are associated with neurodegeneration, pathogen infection, cancer and reduced lifespan. Genetic experiments in model organisms have been critical in determining how autophagy functions in health and disease.

Key Concepts

  • Over 30 atg genes have been shown to regulate autophagy.
  • Autophagy is induced in response to starvation and oxidative stress, enabling cells to recycle macromolecules and degrade damaged organelles.
  • Autophagy is required for steroid‐triggered removal of larval tissues during Drosophila melanogaster development.
  • Autophagosomes can sequester intracellular pathogens, which evade the cell's phagocytic machinery and traffic them to the lysosome for degradation.
  • Decreased autophagy leads to an inability to clear protein aggregates and mutant polyglutamine containing proteins from neurons in fly and worm neurodegeneration models.
  • Induction of autophagy in flies and worms can extend lifespan, whereas its block leads to increased neuronal cell death and reduced lifespan.
  • Autophagy has a context‐dependent role in tumourigenesis.

Keywords: autophagy; Drosophila; C. elegans; zebrafish; S. cerevisiae; neurodegeneration; ageing; cell death; lysosomes

Figure 1. Regulation of autophagy. (a) Steps of autophagy include the formation and expansion of the phagophore (also called isolation membrane) that gives rise to the autophagosome. In yeast, the PAS (phagophore assembling site, an organelle similar to the omegasome in mammalian cells) represents the place in which phagophore formation takes place, with the help of membranes coming from a multitude of organelles. Phagophore maturation and subsequent fusion with the lysosome generates a degradative organelles called autolysosome. Autophagosomes can also fuse with multivesicular endosomes to form amphisomes that eventually fuse with lysosomes. (b) Upon stress stimuli, such as starvation, specific Atg protein complexes are recruited to the PAS to form a phagophore in a hierarchical manner. The first complex is constituted by Atg11, Atg13, Atg17, Atg29 and Atg31 and Atg1, a protein kinase fundamental for autophagosome formation and viability during starvation. The interaction between Atg1 and Atg13 within the complex is either controlled by the serine/threonine kinase, target of rapamycin (TOR), 5' AMP‐activated protein kinase (AMPK) and the protein kinase A (PKA) or it is constitutive. In yeast, under nutrient‐rich conditions, TOR and PKA phosphorylate Atg13 in different sites, reducing its binding affinity for Atg1, while in response to nutrient starvation, TOR and PKA become inactivated, alleviating repression of Atg13. In addition, PKA also phosphorylates directly Atg1, or inhibits AMPK. Atg1 acts upstream of two conserved ubiquitin‐like conjugation pathways that are necessary for phagophore expansion. In particular, Atg7 was identified as an E1‐like enzyme that activates Atg12 and Atg8 in two distinct conjugation pathways. Atg12 and Atg8 are then covalently conjugated to the E2‐like proteins Atg10 and Atg3. This is followed by conjugation of Atg12 to Atg5 which together interact with Atg16. Atg16 acts in part as an E3 ligase for Atg8 lipidation with phosphatidylethanolamine (PE). The amount of Atg8 regulates the size of the autophagosome and Atg16 positive structures undergo a series of homotypic fusion events that expand the phagophore membrane. When a closed double membrane organelle is formed, the phagophore becomes an autophagosome. One of the last step of maturation is the Atg4‐dependent cleavage of Atg8‐PE (deconjugation), an event that triggers Atg12–Atg5–Atg16 complex disassembly. Atg positive autophagosomes are now ready to fuse their outer membrane with that of a lysosome and to release their content into the lysosomal lumen, where it will be degraded. Several other proteins regulating intracellular trafficking compartments also control autophagy. A first example of such dual use involves several vacuolar protein sorting (vps) proteins. First identified as Vps30, Atg6 was found to interact in two distinct complexes, both of which include the class III phosphatidylinositol (PI) kinase (PI3K), Vps34 and Vps15. A complex including Atg6 (in mammals Beclin1), Vps34, Vps15 (human P150) and Vps38 (human UVRAG) is required for vacuolar protein sorting, whereas a second complex containing Atg6, Vps34, Vps15 and Atg14 localises to the PAS and is required for autophagosome formation. In fact, Vps34 converts PI into PI(3)Phosphate (PtdIns3P), a modification that is key to recruitment Atg18, a component of the Atg9 complex, together with Atg2. The role of ESCRTs, SNAREs, HOPs, Tfeb and V‐ATPase as part of the LYNUS machinery in the autophagy process is discussed in detail in the text.
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Mastrodonato, Valeria, Morelli, Elena, and Vaccari, Thomas(Nov 2016) Autophagy in Nonmammalian Systems. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021582.pub2]