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If you haven’t yet read An Introduction to Autophagy, I recommend doing so in order to have the requisite background to follow this post. If you’re already an autophagy connoisseur, then dive right in!

Macroautophagy, most commonly referred to simply as autophagy, can be broadly divided into two categories: selective and non-selective autophagy (1). Bulk autophagy is a non-selective process triggered by nutrient starvation and results in the indiscriminate uptake of cytosolic components by autophagosomes. This self-preservation instinct is critical for survival in times of stress because it serves as an alternate energy source. Recall from the first article in this series that autophagosomes join forces with lysosomes to become autolysosomes. Within these autolysosomes is where digestive enzymes break down suboptimal cytosolic components, recycling macromolecules into building blocks that can be reutilized to drive growth and development. Containing this reaction within vesicles ensures other cellular components are not damaged by the hydrolytic enzymes. 

Selective autophagy, as one might deduce from the name, involves a more targeted approach (1). Specific forms of selective autophagy include mitophagy, lysophagy, ER-phagy, ribophagy, aggrephagy, and xenophagy. Don’t get too bogged down by the names; they merely indicate the type of cargo being engulfed and destroyed. Selective autophagy is associated with cellular quality control and is initiated only when particular receptors bind the nefarious cargo in conjunction with ubiquitin to drive the onset of autophagy. Ubiquitin regulates a number of cellular functions by flagging particular molecules that deserve attention. It thereby behaves as a signal, catching the attention of receptors that are designed to handle various substrates (2). In autophagy, attachment of ubiquitin (or so-called ubiquitination) causes recognition of a substrate by a receptor capable of recruiting the autophagic machinery, thereby instigating destruction. 

If you’re old enough to remember the days of physical boarding passes, you are probably all too familiar with the pit-in-your-stomach sensation upon seeing the infamous, dreaded stamp for additional screening. Ubiquitination in the context of autophagy is like an investigator that has identified a suspect. Only once the cargo has been screened and determined dangerous will receptors pick it up. The neat thing about ubiquitination is that it is reversible, enabling dynamic and spatiotemporal regulation of cell signaling and protein breakdown. That means that if Mr. Ubiquitin was wrong in his assessment, the suspect can be released. Describing this any more is outside the scope of this brief description, but worth mentioning nonetheless I think! 

Now let’s dive into a few of the more well-studied forms of selective autophagy. 

Mitophagy is characterized by mitochondrial autophagy (1). Mitochondria are the engines within each cell, supplying critical energy that drives cellular processes. Inefficient mitochondria release noxious molecules that damage DNA and cause inflammation. PINK1 and Parkin are the directors of ubiquitination of injured mitochondria, assuring that only non-functional mitochondria are eradicated. PINK1 is normally imported into the mitochondria by a set of carriers. However, damaged mitochondria exhibit impaired import of PINK1, allowing it to accumulate on the outer membrane. PINK1 subsequently attracts and activates Parkin, which goes on to induce ubiquitination. Various receptors recognize this ubiquitination and call the autophagic machinery to action. 

Lysophagy is a second important form of selective autophagy where the target is injured lysosomes (1). As we have learned, lysosomes house toxic hydrolytic enzymes that are ideal for molecule breakdown, but dangerous if they somehow manage to escape from the lysosome. Deterioration of the lysosomal membrane permits leaking of the hydrolytic enzymes and eventual cell death. Galectins are the primary mediators of lysophagy, and are recruited to the lumen of lysosomes ultimately initiating ubiquitination. Once again, specific receptors recognize this tag and attract autophagic complexes for lysosomal destruction. 

Next we have aggrephagy, the pathway by which cells clear protein aggregates (1). Proteins become sticky and produce tangles that are toxic to the cell when any one of their structural tiers becomes disrupted. Recall from An Introduction to Autophagy that proteins are composed of four distinct structures, all of which dictate their function. A number of receptors are involved in detecting these aggregates and signaling their demise. One such receptor is p62. Ubiquitin will tag misfolded proteins, subsequently making them attractive to the p62 receptor (1). This complex of misfolded protein, ubiquitin, and p62 serves to recruit the autophagic machinery, sequestering and breaking down the protein into its components. 

The final method of selective autophagy that I will cover is that of xenophagy (1). Xenophagy is critical in protecting us from bacterial invasion, as this mechanism involves capture of pathogens in the cytoplasm. Xenophagy works in concert with the immune system to eliminate foreign invaders. Virophagy is a similar process specific to the destruction of viruses.  Xenophagy is a unique form of selective autophagy as it targets external or alien threats as opposed to components of the cell itself (1). Xenophagy is insufficient to completely obliterate bacterial proliferation as some bacteria have evolved a system to block autophagosome formation or to neutralize hydrolytic enzymes within lysosomes. Once inside the cytosol of a cell, bacteria can be labeled with ubiquitin and galectins, facilitating detection by receptors (such as p62 and NDP52) and instigating autophagy. Interestingly, there may be a role of autophagy in antigen presentation to immune cells which promotes the defense against viruses (1). 

Other methods of selective autophagy include ER-phagy (selective autophagy of subregions of the ER membrane), pexophagy (autophagy of damaged peroxisomes), ferritinophagy (selective autophagy of ferritin), glycophagy (selective autophagy of glycogen), lipophagy (selective autophagy of lipid droplets), and nucleophagy (selective autophagy of nuclear material) (1, 3). These are relatively novel, emerging pathways of selective autophagy that are just being elucidated.  

In summary, while non-selective autophagy is largely induced by nutrient stress, selective autophagy is a more articulated process by which damaged cellular components or external invaders are captured and destroyed before they are able to wreak havoc. One consistently observed strategy of selective autophagy is the tagging with ubiquitin of nefarious cargo that causes binding of receptors and consequent recruitment of autophagic machinery (1). However, it has been discovered that ubiquitin is not always a necessary signal to induce autophagy, but this pathway is currently not well understood. The therapeutic potential of targeting the receptors that initiate autophagy is under investigation in the prevention or treatment of diseases characterized by disrupted autophagy. This will be the topic of the next post!

Takeaway points

• There are two key autophagic processes: selective and non-selective.
• In both types of autophagy, autophagosomes engulf cellular content before fusing with lysosomes at which point hydrolytic enzymes digest the cargo. 
• Non-selective autophagy happens constantly at a basal level and is upregulated in times of nutrient distress. Cytoplasmic components, such as damaged organelles and macromolecules, are degraded and their amino acids recycled to replenish the amino acid pool. 
• Selective autophagy involves tagging and subsequent recognition of harmful cargos, such as bacteria.
• Selective autophagy generally involves the process of 1) threatening cargo identification, 2) cargo tagging (often by ubiquitin), 3) receptor recognition, 4) autophagic machinery recruitment, 5) component digestion. 
• Ubiquitin is a commonly employed ‘tag’ that serves as a danger signal. It attaches to cellular components that it has identified as problematic. 
• Specific receptors recognize ubiquitin and latch onto these ubiquitin-cargo complexes. 
• These receptors recruit autophagic machinery for lysosomal degradation and component recycling. 
• Non-ubiquitin dependent autophagy may also occur, although this process is not currently well established. 
• Various forms of selective autophagy exist based on the targeted component. 

References

1. Vargas JNS, Hamasaki M, Kawabata T, Youle RJ, Yoshimori T. The mechanisms and roles of selective autophagy in mammals. Nature Reviews Molecular Cell Biology. Published online October 27, 2022:1-19. doi:10.1038/s41580-022-00542-2
2. Yin Z, Popelka H, Lei Y, Yang Y, Klionsky DJ. The Roles of Ubiquitin in Mediating Autophagy. Cells. 2020;9(9):2025. doi:10.3390/cells9092025
3. Papandreou ME, Konstantinidis G, Tavernarakis N. Nucleophagy delays aging and preserves germline immortality. Nature Aging. Published online December 23, 2022. doi:10.1038/s43587-022-00327-4