An overview of macroautophagy in yeast

Abstract

Macroautophagy is an evolutionarily conserved dynamic pathway that functions primarily in a degradative manner. A basal level of macroautophagy occurs constitutively, but this process can be further induced in response to various types of stress including starvation, hypoxia and hormonal stimuli. The general principle behind macroautophagy is that cytoplasmic contents can be sequestered within a transient double-membrane organelle, an autophagosome, which subsequently fuses with a lysosome or vacuole (in mammals, or yeast and plants, respectively), allowing for degradation of the cargo followed by recycling of the resulting macromolecules. Through this basic mechanism, macroautophagy has a critical role in cellular homeostasis; however, either insufficient or excessive macroautophagy can seriously compromise cell physiology, and thus, it needs to be properly regulated. In fact, a wide range of diseases are associated with dysregulation of macroautophagy. There has been substantial progress in understanding the regulation and molecular mechanisms of macroautophagy in different organisms; however, many questions concerning some of the most fundamental aspects of macroautophagy remain unresolved. In this review, we summarize current knowledge about macroautophagy mainly in yeast, including the mechanism of autophagosome biogenesis, the function of the core macroautophagic machinery, the regulation of macroautophagy and the process of cargo recognition in selective macroautophagy, with the goal of providing insights into some of the key unanswered questions in this field.

Keywords: autophagosome biogenesis; autophagy; cargo recognition; regulation; stress.

Figure 1. A model of the different stages of autophagy in yeast

In yeast, macroautophagy can be generally divided into the following stages: induction, nucleation, expansion and completion, docking and fusion, and finally degradation and efflux. The Atg proteins form most of the primary machinery that function in each of these stages.

Figure 2. Different membrane sources of autophagosome formation

The formation of the phagophore and the double-membrane autophagosome are the distinguishing morphological hallmark of macroautophagy in yeast. Several membrane donors including the plasma membrane, ER, ER exist site (ERES), mitochondria, and the Golgi apparatus may contribute to the biogenesis of the phagophore and autophagosome in yeast. In mammalian cells an additional structure, the omegasome, forms directly from the ER membrane, but the relationship between the omegasome and phagophore is not clear.

Figure 3. The interactome of the Atg1 kinase complex

Upon autophagy induction, the Atg1 complex is mainly composed of three components: Atg1, Atg13 and the Atg17-Atg31-Atg29 subcomplex. Atg13 can bind to Atg1 and the Atg17-Atg31-Atg29 subcomplex directly, whereas there is no known binding site on Atg1 for the subcomplex. The scaffold protein Atg11, which plays a critical role under growing conditions and for selective autophagy, interacts the with Atg1 kinase complex by binding to Atg1, Atg17 and Atg29.

Figure 4. The Atg9 complex

The transmembrane protein Atg9 can reside at the PAS and peripheral structures proximal to mitochondria. With the help of Atg11, Atg23, Atg27 and Atg41, Atg9 can travel from the peripheral structures to the PAS, playing a role in orchestrating membrane delivery. Retrograde movement relies on the Atg2-Atg18, Atg1-Atg13 and Atg14-containing PtdIns3K complexes.

Figure 5. Two ubiquitin-like conjugation systems

The two ubiquitin-like proteins Atg8 and Atg12 are used to generate the conjugation products Atg8-PE and Atg12-Atg5-Atg16, respectively. These two Ubl conjugation systems use the same E1-like enzyme Atg7, but different E2-like enzymes, Atg3 for Atg8 and Atg10 for Atg12. Furthermore, the Atg12-Atg5-Atg16 complex can work as an E3-like enzyme for Atg8-PE formation.

Figure 6. A general model of selective autophagy in yeast

For different kinds of selective autophagy in yeast there is a commonly used model to allow cargo recognition. This schematic depicts three kinds of selective autophagy: Cvt pathway, mitophagy, and pexophagy. Detailed information is provided in the corresponding table.