Autophagy

Lysosomes are membrane-bound organelles responsible for the degradation of various biological macromolecules. Vesicles containing hydrolytic enzymes bud from the Golgi and fuse with endosomes to form the mature lysosome capable of breaking down various types of cargo. Their general function in recycling biological molecules places lysosomes at center of various processes including autophagy, endyocytosis, and phagocytosis.

During cellular stress the protein folding capacity of the ER is diminished. In order to maintain homeostasis and ensure proper protein folding cells activate the unfolded protein response (UPR), a signaling network consisting of sensors and effectors to enhance the chaperone activity of the cell, increase degradation of accumulated proteins, and/or trigger apoptosis.  Inositol-requiring enzyme 1 (IRE1), an ER-transmembrane protein, is an essential component of the UPR pathway important for sensing and responding to ER stress.

Autophagy is important for the removal of damaged organelles or proteins as well as for the regulation of cellular homeostasis in response to stress. Proteins or organelles that are targeted for degradation are engulfed in a double-membrane structure called the autophagosome that eventually fuses with the lysosome to mediate cargo degradation. Atg5 plays an important regulatory role in the early steps of this process.

Autophagy is an essential cellular process that maintains homeostasis through the degradation and recycling of cytoplasmic organelles and macromolecules. Substrates targeted for autophagy are engulfed in a double-membrane structure called the autophagosome which is then targeted to the lysosome for degradation. The initiation of autophagy requires two separate ubiquitin-like protein (UBL) systems that regulate autophagosome assembly. In these systems Atg7 acts as an E1-like enzyme for the UBLs Atg12 and Atg8.

During autophagy ubiquitinated cargo or substrates are engulfed in a double-membrane autophagosome and transported to the lysosome for degradation. This process is important for maintaining cellular homeostasis and for degrading damaged organelles or misfolded protein aggregates. p62, also known as sequestosome 1 (SQSTM1), is an autophagy receptor that recognizes and recruits cargo to the autophagosome through its interaction with Atg8.

Heat shock cognate 71 kDa protein (Hsc70), also known as HSPA8, is a member of the heat shock protein 70 family (Hsp70). Unlike Hsp70, it is a constitutively expressed chaperone protein and is involved in diverse cellular processes including protein folding and protein degradation. Hsc70 consists of two domains: the nucleotide binding domain (NBD) and the substrate binding domain (SBD). Hsc70, with the help of accessory proteins, exerts its chaperone activity by binding to short hydrophobic stretches of nascent or unfolded polypeptides through the SBD in an ATP-dependent manner.

Atg12 is a ubiquitin-like protein that plays an essential role in cellular homeostasis by regulating the degradation and recycling of cytoplasmic organelles and macromolecules. Atg12 is one of two ubiquitin-like protein systems that is required during the early steps of autophagosome formation. Upon the initiation of phagopore assembly Atg12 is activated by binding to the E1-like enzyme Atg7 and is then transferred to the E2 enzyme Atg10.

Atg9 is the only essential transmembrane protein involved in cellular autophagy. Autophagy regulates cellular homeostasis by allowing the turnover and recycling of misfolded proteins and damaged organelles. Formation of the double-membrane isolation membrane that forms the pre-autophagosome requires the contribution of highly mobile cytoplasmic vesicles containing Atg9. These vesicles are derived from recycling endosomes and are responsible for recruiting and delivering lipid components to the assembling autophagosome.

Microtubule-associated protein-1 light chain 3 (LC3/LC3B) is a ubiquitin-like protein involved in the formation of the autophagosome. It is homologous to the yeast Atg8 protein. Autophagosomes are important for the degradation and recycling of intracellular cargo such as misfolded proteins or damaged organelles. Upon induction of autophagy, LC3 is conjugated to the lipid phosphatidylethanolamine (PE) by the Atg12-Atg5-Atg16 protein complex.

The mammalian target of rapamycin (mTOR) signaling pathway allows cells to monitor environmental signals like nutrient availability and oxygen levels. mTOR is a phosphoinositide 3-kinase (PI3K)-related protein that assembles into large protein complexes (mTORC1 and mTORC2) capable of regulating cell metabolism, growth, and proliferation.