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Alterations in the process of autophagy are involved in almost every degenerative disease affecting middle-aged and elderly adults.

A cell that forms the basic structural and functional unit of every organism is constantly undergoing thousands of molecular processes that collectively help in maintaining life.

During these activities, errors may lead to the formation of faulty cell components, or the existing cellular components may get old, damaged, or worn out. Moreover, in nutrient-limiting conditions, the cell may not have resources or vital building blocks that are required to synthesize the molecules necessary for maintaining the appropriate energy levels and sustaining life in the cell.

Under such circumstances, a eukaryotic cell resorts to one of the most fascinating and evolutionarily conserved processes called autophagy. This is the process by which the cell can degrade some of its components, and use the resulting building blocks to synthesize new ones.

Let us understand in more detail how autophagy occurs in a cell, and which cellular components and organelles bring about this process.

How Autophagy Takes Place in a Cell

The process of autophagy is initiated in response to molecular triggers that indicate damage, starvation, oxidative stress, or pathogenic invasion. The components to be recycled are marked and targeted for degradation by lysosomes. These are small spherical organelles that comprise an acidic interior containing a set of digestive enzymes.

Depending on the precise pathway followed to introduce the targeted components into the lysosomes, autophagy has been classified as macroautophagy, microautophagy, and chaperone-mediated autophagy. Each of these have been explained below.

Macroautophagy
This is the main pathway for autophagy, and hence, the word 'autophagy' is often used synonymously with 'macroautophagy.' It involves bulk degradation of organelles and proteins that are introduced into the lysosome through specialized vesicles.

Macroautophagy

Step 1The conditions of starvation are sensed by a protein called TOR (target of rapamycin), which is responsible for regulating the metabolism and protein synthesis inside the cell. In the absence of nutrients, growth factors, or oxygen, the activity of TOR is inhibited, which leads to the induction of macroautophagy in the cell.

Step 2In response to such induction, a double-layered membrane called phagophore or isolation membrane begins to form in the cytosol. Several proteins and lipid molecules participate in the formation of phagophore, at the right site of the cytosol and around the right cellular components.

Step 3This membrane further elongates to surround the cargo targeted for degradation, which generally includes some part of the cytosol, certain long-lived or damaged proteins, and old or damaged organelles. The extreme ends of the membrane fuse together to form a double-membrane vesicle, which is termed autophagosome.

Step 4Once the autophagosome is formed, the proteins that participated in building the membrane are released into the cytosol. These proteins are then free to assist the formation of new phagophores, whenever required.

Step 5The function of this auophagosome is to fuse with, and deliver the cargo into the lysosomes. The outer layer of the autophagosome membrane fuses with the lysosomal membrane, thus, releasing a single-layered vesicle into the lysosome. The digestive enzymes present in the lysosomes degrade the single-layered membrane, and the lysosome is now termed as autolysosome.

Step 6The inner cargo is now exposed to the lytic enzymes, like proteases, lipases, and hydrolases. These enzymes break down the cargo into basic building blocks, like amino acids, sugars, other carbohydrate moieties, as well as certain lipid molecules. These are then released into the cytosol for building new molecules, and they are used as an energy source to fuel metabolic processes of the cells.

Microautophagy
This mechanism of autophagy involves the direct entry of targeted cellular components into the lysosomes. Cytosolic molecules, like glycogen, protein aggregates, misfolded proteins, and organelles may be degraded through microautophagy.

Microautophagy

Step 1The process begins with the formation of tubular invagination of the lysosome. The lysosomal membrane forms tube-like projections that surround the targeted molecule or organelle.

Step 2The surrounding membrane projections fuse together to form an intralysosomal vesicle that contains the cargo. The lytic enzymes can now degrade this cargo, and the building blocks are released into the cytosol.

Step 3A special case of microautophagy is micronucleophagy or piecemeal microautophagy of the nucleus, during which a part of the nucleus is sequestered and degraded.

Chaperone-mediated Autophagy (CMA)
This route of autophagy functions to degrade only a specific set of misfolded, or erroneously formed cytosolic proteins. The proteins are identified and guided into the lysosome through cytosolic molecular assistants called chaperones.

Chaperone-mediated autophagy

Step 1The proteins to be degraded through the CMA contain a unique motif that is biochemically related to the pentapeptide KFERQ. When the protein is not correctly folded, or is damaged, this motif gets exposed and is recognized by a molecular chaperone called hsc70 (heat shock cognate protein of 70KDa). Hsc70 binds to this unique motif and guides the protein, or CMA substrate, to the lysosomal surface.

Step 2The lysosomal surface has a protein called lysosome-associated membrane protein type 2A (LAMP-2A), embedded into its membrane. This protein serves as a receptor for the substrate-hsc70 complex.

Step 3Once the substrate-hsc70 complex binds to the LAMP-2A monomer, hsc70 as well as other membrane molecules and chaperones, like hsp90 (heat shock protein 90) unfold the substrate protein. Also, the LAMP-2A protein undergoes conformational changes and multimerization to form a hollow, cylindrical transport structure called CMA translocation complex.

Step 4The unfolded substrate passes through the translocation complex and enters the lysosomal lumen. A variant of the hsc70, called lysosomal hsc70, is present in the lumen of the lysosome. It helps in pulling the substrate inside the lysosome, and it also prevents it from returning to the cytosol.

Step 5Once the substrate passes into the lysosomal lumen, the CMA translocation complex is immediately disassembled by hsc70, hsp 90, and other proteins present at the lysosomal membrane. The substrate is degraded by proteases present in the lumen, and the resultant amino acids are released into the cytosol.

Autophagy and Cell Death

Autophagy is known to be a cell survival mechanism, and has been shown to inhibit programmed cell death or apoptosis (a form of cellular suicide). However, certain experiments have demonstrated the induction of cell death by macroautophagy, thereby, suggesting it to be one of the mechanisms through which cells commit suicide. It is characterized by bulk degradation of key proteins or organelles that are essential for survival of the cell and an accumulation of several autophagosomes inside the cell. Such cell death is termed as autophagic cell death (ACD). However, the precise mechanisms that lead to ACD as well as the connection between autophagy and apoptosis is not yet clear.

Autophagy plays a vital role in several physiological processes, like tissue repair, maintaining cellular and tissue homeostasis, as well as aging. Alterations in autophagic pathways have been associated with several muscular and neurodegenerative disorders, deterioration of heart muscles, as well as certain types of cancers. Its precise role in cell survival and cell death is being explored extensively.