Autophagy is an intracellular phenomenon that is activated under conditions of intracellular and extracellular modalities of stress such as endoplasmic (ER) stress or nutrient deprivation/starvation. This phenomenon is characterized by the presence of double membrane cytosolic vacuoles called “autophagosomes.” The autophagosomes have been documented to engulf and sequester cytosolic organelles under conditions of stress and ultimately fuse with the lysosomes. The lysosomal hydrolases then breakdown the organelles and recycle the proteins and amino acids into the cell machinery for its survival in nutrient compromised conditions. Autophagy has been documented to be a highly conserved phenomenon from yeast to mammals. A common unified nomenclature has been proposed to name the proteins involved in the process of autophagy. The genes involved in mammalian autophagy are denoted as ‘ATG-genes’ while the proteins are depicted as ‘atg-proteins’. Also a very recent report suggests and outlines the guidelines for the interpretation and the use of assays used to study autophagy in higher eukaryotes. Thus the studies in atuophagy are gaining momentum and becoming more structured.
Though autophagy has been documented to assist cell survival, prolonged periods of autophagy induction have been recently suggested to be responsible for another type of cell death called “autophagic cell death” (type II). Autophagic cell death is considered as a programmed cell death as its execution involves a sequential activation of a number of enzymes and autophagy proteins. Growth factor or nutrient deprivation mediated autophagic cell death has been documented in neuronal cell culture systems. Autophagic cell death, a conserved integral pathway involved in mammalian cell development is also activated under certain pathological conditions such as the neurodegenerative diseases. Also, the activity of autophagosomes during prolonged periods of autophagy induction might end in the sequestration and degradation of seminal cell organelles such as the mitochondria resulting in cell death.
Classification of Autophagy
Autophagy is classified into 3 types: 1) macroautophagy, 2) microautophagy and 3) chaperone-mediated autophagy.
Macroautophagy: It is the main route for bulk protein degradation under conditions of stress and starvation. Macroautophagy is a multi-step process and involves the formation of a double membraned vesicular structure called the autophagosome and is presumably derived from the endoplasmic reticulum (ER). Autophagosomes engulf cytoplasmic components including whole organelles and transport them to the lysosomes. Once it reaches the lysosome, the outer membrane of the autophagosome fuses with the membrane of the lysosome and matures into a structure known as the “autophagolysosome.” The vesicle transported into the lysosome delivers its contents following the disintegration of its membrane. The vesicular contents are then broken down into amino acids and recycled into the protein machinery of the cell to sustain survival under nutrient deprivation conditions. Recently, mammalian proteins involved in the process of macroautophagy have been identified and unified under a single nomenclature. Some of the proteins well known include Atg8, Atg6, Atg7, Atg12 and Atg5 demonstrates the processes involved in macroautophagy. Since macroautophagy is the predominant form observed, it is often referred to as autophagy.
Microautophagy: In this process internalization of the proteins is made directly through the lysosomal membrane by invagination of the membrane at different locations forming a multivesicular body. It is non-selective and has an inherently basic activation level in the cell. Thus microautophagy seems to be activated even under normal conditions unlike macroautophagy.
Chaperone-mediated autophagy: This process is restricted to elimination of proteins that possess an amino acid sequence biochemically related to the pentapeptide Lys-Phe-Glu-Arg-Gln (KFERQ) during conditions of prolonged starvation. The proteins are tagged by the heat shock cognate (hsc-73) protein of 73 kDa and binds to a lysosome membrane receptor LAMP-2a which facilitates the entry of the complex into the lysosome for degradation purposes.
Autophagy is characterized by the formation of autophagosomes. Formation of autophagosomes is a well regulated process involving a number of proteins, some of which is mentioned above. One of the main proteins which control the formation of these double membraned vesicles is the mammalian target of rapamycin (mTOR). The TOR proteins are assigned to a protein family termed the phosphatidylinositol kinase related kinases (PIKKs) and function as Ser/Thr protein kinases. This protein is sensitive to the nutrient levels in the cell and is a regulator of autophagy. Under normal/healthy conditions, mTOR is hyperphosphorylated and exerts an inhibitory influence on the activation of the autophagy proteins. Under starvation conditions, this inhibitory influence is lifted and the phosphorylation state of the Atg13 changes (hypophosphorylated) which then effectively binds to the Atg1 protein and initiates a cascading set of events resulting in the induction of autophagy.
Autophagosome formation, once initiated after nucleation from the endoplasmic reticulum (ER), undergoes a series of steps towards its maturation. The process is similar to the ubiquitinproteosome pathway. One of the autophagosome proteins, Atg12, is conjugated to Atg7 (E1-like) and then to Atg10 (E2-like) forming thioester intermediates through its COOH-terminal glycine. Finally, Atg12 conjugates to Atg5 via an internal lysine residue in the latter. Atg16 then binds to this conjugate non-covalently and dimerizes with another Atg12-Atg5-Atg16 complex to form a complex required for autophagosome formation. Recent reports illustrate the co-localization of the Atg12-Atg5 protein complex with LC3 (mammalian orthologue of Atg8).