Mitophagy

Mitophagy is the selective degradation of

Organelles and bits of cytoplasm are sequestered and targeted for degradation by the lysosome for hydrolytic digestion by a process known as autophagy. Mitochondria metabolism leads to the creation of by-products that lead to DNA damage and mutations. Therefore, a healthy population of mitochondria is critical for the well-being of cells. Previously it was thought that targeted degradation of mitochondria was a stochastic event, but accumulating evidence suggest that mitophagy is a selective process.[6]

Generation of ATP by oxidative phosphorylation leads to the production of various reactive oxygen species (ROS) in the mitochondria, and submitochondrial particles. Formation of ROS as a mitochondrial waste product will eventually lead to cytotoxicity and cell death. Because of their role in metabolism, mitochondria are very susceptible to ROS damage. Damaged mitochondria cause a depletion in ATP and a release of cytochrome c, which leads to activation of caspases and onset of apoptosis. Mitochondrial damage is not caused solely by oxidative stress or disease processes; normal mitochondria will eventually accumulate oxidative damage hallmarks overtime, which can be deleterious to mitochondria as well as to the cell. These faulty mitochondria can further deplete the cell of ATP, increase production of ROS, and release proapoptopic proteins such as caspases.

Because of the danger of having damaged mitochondria in the cell, the timely elimination of damaged and aged mitochondria is essential for maintaining the integrity of the cell. This turnover process consists of the sequestration and hydrolytic degradation by the lysosome, a process also known as mitophagy.

Mitochondrial depletion reduces a spectrum of senescence effectors and phenotypes while preserving ATP production via enhanced glycolysis.^[7]

Pathways

In mammals

There are several pathways by which mitophagy is induced in mammalian cells. The

In unhealthy mitochondria, the inner mitochondrial membrane becomes depolarized. This membrane potential is necessary for the TIM-mediated protein import. In depolarized mitochondria, PINK1 is no longer imported into the inner membrane, is not cleaved by PARL and PINK1 concentration increases in the outer mitochondrial membrane. PINK1 can then recruit Parkin, a cytosolic E3 ubiquitin ligase.^[9] It is thought that PINK1 phosphorylates Parkin ubiquitin ligase at S65 which initiates Parkin recruitment at the mitochondria.^[10][11] The phosphorylation site of Parkin, at S65, is homologous to the site where ubiquitin is phosphorylated. This phosphorylation activates Parkin by inducing dimerization, an active state. ^{[citation needed]} This allows for Parkin-mediated ubiquitination on other proteins.^[10]

Because of its PINK1-mediated recruitment to the mitochondrial surface, Parkin can ubiquitylate proteins in the outer mitochondrial membrane.

Other pathways that can induce mitophagy includes mitophagy receptors on the outer mitochondrial membrane surface. These receptors include NIX1, BNIP3 and FUNDC1. All of these receptors contain LIR consensus sequences that bind LC3/GABARAP which can lead to the degradation of the mitochondria. In hypoxic conditions BNIP3 is upregulated by HIF1α. BNIP3 is then phosphorylated at its serine residues near the LIR sequence which promotes LC3 binding. FUNDCI is also hypoxia sensitive, although it is constitutively present at the outer mitochondrial membrane during normal conditions. ^[10] Mitophagy can also be artificially introduced by a series of synthetic autophagy receptors^[13] that are composed of antibody fragments to recognize the mitochondrial outer membrane proteins.^[14]

In

Mitophagy in yeast was first presumed after the discovery of Yeast Mitochondrial Escape genes (yme), specifically yme1. Yme1 like other genes in the family showed increase escape of mtDNA, but was the only one that showed an increase in mitochondrial degradation. Through work on this gene which mediates the escape of mtDNA, researchers discovered that mitochondrial turnover is triggered by proteins.[18]

More was discovered about genetic control of mitophagy after studies on the protein UTH1. After performing a screen for genes that regulate longevity, it was found in ΔUTH1 strains that there was an inhibition of mitophagy, which occurred without affecting autophagy mechanisms. This study also showed that the Uth1p protein is necessary to move mitochondria to the vacuole. This suggested there is a specialized system for mitophagy. Other studies looked at AUP1, a mitochondrial phosphatase, and found Aup1 marks mitochondria for elimination.^[18]

Another yeast protein associated with mitophagy is a mitochondrial inner membrane protein, Mdm38p/Mkh1p. This protein is part of the complex that exchanges K+/H+ ions across the inner membrane. Deletions in this protein causes swelling, a loss of membrane potential, and mitochondrial fragmentation.^[18]

Recently, it has been shown that ATG32 (autophagy related gene 32) plays a crucial role in yeast mitophagy. It is localized to the mitochondria. Once mitophagy is initiated, Atg32 binds to Atg11 and the Atg32-associated mitochondria are transported to the vacuole. Atg32 silencing stops recruitment of autophagy machinery and mitochondrial degradation. Atg32 is not necessary for other forms of autophagy.^[19][20]

All of these proteins likely play a role in maintaining healthy mitochondria, but mutations have shown that dysregulation can lead to a selective degradation of mitochondria. Whether these proteins work in concert, are main players in mitophagy, or members in a larger network to control autophagy still remains to be elucidated.

Role in the immune response

Mitochondria play an important role in the functioning of the immune system. Mitochondrial damage-associated molecular patterns (DAMPs) such as parts of damaged organelles or mtDNA are secreted by cells following sterile inflammation, dysregulations in cell metabolism, or infection. There is evidence that these DAMPs act as one of the key triggers of the innate immune response. Mitophagy provides the elimination of non-functioning mitochondria and maintains mitochondrial homeostasis. Due to that, it can be seen as an immunomodulatory tool to keep the immune response in check.^[21]

Hematopoiesis

In addition to immunomodulatory functions, mitophagy can regulate the fate of hematopoietic stem cells (HSC). Mitophagy impaired due to the deletion of autophagy-related genes led to a loss of HSC function, more likely as a result of mitochondrial damage that stimulated excessive ROS production. On the contrary, mitophagy induction appeared to be protective for HSC and directed stem cell differentiation to the myeloid lineage.^[22]

Macrophages

Immune cell activation and the change in phenotype are followed by metabolic reprogramming. Activated cells, including

It is also important to mention that mitophagy impairment in macrophages is quite common in the early stages of different pathological states. Macrophages play an important role in the innate immune response. However, conditions leading to immune paralysis, e.g. sepsis, make them incapable of efficient bactericidal clearance. Hence, some studies highlighted the role of mitophagy as a biomarker of different stages of sepsis, as it is inhibited in the early stage and induced later.^[24] Other reports showed compromised mitophagy in experimental and human kidney fibrosis. Some mitophagy-associated molecules such as Mfn2 and Parkin are negatively regulated in this pathological state. Consequently, the frequency of regulatory profibrotic M2 macrophages was higher, confirming the role of mitophagy in the induction of the pro-inflammatory M1 phenotype.^[24][25]

Inflammasome

Many studies demonstrate that the release of mtROS and mtDNA as DAMPs plays a crucial role in the activation of the inflammasome and following inflammation mediated by IL-1β. NF-κB, a protein complex that is important for immune cell signaling, but also plays an important role in mitophagy induction, has been reported to control the activation of the inflammasome by adopting the p62-mitophagy pathway.^[26]

The importance of mitophagy was demonstrated by the deletion of

It is known that some viruses can modulate mitophagy (directly or indirectly) using different mechanisms and, as a result, cause a disbalance in the innate immune response.[21] mtDNA that exits damaged mitochondria acts as one of the triggers of type I interferon (IFN I) production. Some viruses can induce mitophagy and therefore inhibit the production of these crucial antiviral cytokines. There are reports of viral proteins directly or indirectly interacting with autophagy and mitophagy-associated proteins such as LC3 or Pink1-Parkin and usurping them to trigger mitophagy and subsequently inhibit IFN I responses.^[21][30]

Mitochondria is a dynamic structure regulating its morphology by context-dependent constant fission and fusion. Fission is crucial for mitophagy, as it cuts off a small mitochondrial part that can be further engulfed by the autophagosome.^[31] The viruses Hepatitis B (HBV) and hepatitis C (HCV) take advantage of this mechanism by inducing mitochondrial fission and following mitophagy. HBV stimulates the phosphorylation of Drp1, a fission-promoting GTPase molecule, and the expression and recruitment of Parkin. HCV is known to promote mitophagy by inducing ROS production. Other viruses such as Human Parainfluenza (HPIV3) regulate host immune responses by clearing mitochondrial antiviral-signaling protein (MAVS) located in the outer mitochondrial membrane. There are specific proteins produced by HPIV3 that induce mitophagy in the infected cell, thus promoting MAVS degradation and the corresponding inhibition of IFN I production. The same strategy is used by the SARS-CoV-encoded protein ORF-9b, which triggers the degradation of several mitochondrial proteins, including MAVS.^[32][33]

Relation to disease

Cancer

As of 2020, the role of mitophagy in cancer is not fully understood. Some models of mitophagy, such as PINK1 or

Parkinson's disease is a neurodegenerative disorder pathologically characterized by death of the dopamine-producing neurons in the substantia nigra. There are several genetic mutations implicated in Parkinson's disease, including loss of function PINK1 ^[36] and Parkin.^[9] Loss of function in either of these genes results in the accumulation of damaged mitochondria, and aggregation of proteins or inclusion bodies – eventually leading to neuronal death.

Mitochondria dysfunction is thought to be involved in Parkinson's disease pathogenesis. In spontaneous, usually aging related Parkinson's disease (non-genetically linked), the disease is commonly caused by dysfunctional mitochondria, cellular oxidative stress, autophagic alterations and the aggregation of proteins. These can lead to mitochondrial swelling and depolarization. It is important to keep the dysfunctional mitochondria regulated, because all of these traits could be induced by mitochondrial dysfunction and can induce cell death.^[37] Disorders in energy creation by mitochondria can cause cellular degeneration, like those seen in the substantia nigra.^[31]

Tuberculosis

Tuberculosis is a contagious disease caused by infection with the airborne pathogen Mycobacterium tuberculosis. Recent investigation has shown that chronic infection by Mycobacterium tuberculosis in the lungs or ex-vivo infection by non-pathogenic mycobacteria (M.bovis) elicits activation of the receptor-mediated pathway for mitophagy. Here the receptor mediated mitophagy pathways are elicited through NIX that gets upregulated during M. tuberculosis infection. Elicited NIX/BNIP3L receptor recruitment of LC3 molecules mediating formation of phagophore that engulf defective mitochondria directly ^[38]

References