Mitophagy is the selective degradation of
mitochondria by
autophagy. It often occurs to defective mitochondria following damage or stress. The process of mitophagy was first described over a hundred years ago by
Margaret Reed Lewis
Margaret Adaline Reed Lewis (1881–1970) was an American cell biologist and embryologist who made contributions to cancer research and cell culture techniques, and was likely the first person to successfully grow mammalian tissue ''in vitro''. ...
and
Warren Harmon Lewis.
Ashford and Porter used electron microscopy to observe mitochondrial fragments in liver
lysosomes by 1962,
and a 1977 report suggested that "mitochondria develop functional alterations which would activate autophagy."
The term "mitophagy" was in use by 1998.
Mitophagy is key in keeping the cell healthy. It promotes turnover of mitochondria and prevents accumulation of dysfunctional mitochondria which can lead to cellular degeneration. It is mediated by
Atg32 (in yeast) and
NIX and its regulator
BNIP3 in mammals. Mitophagy is regulated by
PINK1 and
parkin proteins. In addition to the selective removal of damaged mitochondria, mitophagy is also required to adjust mitochondrial numbers to changing cellular metabolic needs, for steady-state mitochondrial turnover, and during certain cellular developmental stages, such as during
cellular differentiation of red blood cells.
Role
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.
Generation of ATP by
oxidative phosphorylation
Oxidative phosphorylation (UK , US ) or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine t ...
leads to the production of various
reactive oxygen species
In chemistry, reactive oxygen species (ROS) are highly reactive chemicals formed from diatomic oxygen (). Examples of ROS include peroxides, superoxide, hydroxyl radical, singlet oxygen, and alpha-oxygen.
The reduction of molecular oxygen ...
(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
caspase
Caspases (cysteine-aspartic proteases, cysteine aspartases or cysteine-dependent aspartate-directed proteases) are a family of protease enzymes playing essential roles in programmed cell death. They are named caspases due to their specific cyst ...
s 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
Senescence () or biological aging is the gradual deterioration of functional characteristics in living organisms. The word ''senescence'' can refer to either cellular senescence or to senescence of the whole organism. Organismal senescence inv ...
effectors and phenotypes while preserving ATP production via enhanced
glycolysis.
Pathways
In mammals
There are several pathways by which mitophagy is induced in mammalian cells. The
PINK1 and
Parkin pathway is, so far, the best characterized. This pathway starts by deciphering the difference between healthy mitochondria and damaged mitochondria. A 64-kDa protein, PTEN-induced kinase 1 (PINK1), has been implicated to detect mitochondrial quality. PINK1 contains a
mitochondrial targeting sequence (MTS) and is recruited to the mitochondria. In healthy mitochondria, PINK1 is imported through the outer membrane via the
TOM complex, and partially through the inner mitochondrial membrane via the
TIM complex
The translocase of the inner membrane (TIM) is a complex of proteins found in the inner mitochondrial membrane of the mitochondria
A mitochondrion (; ) is an organelle found in the Cell (biology), cells of most Eukaryotes, such as animals, ...
, so it then spans the inner mitochondrial membrane. The process of import into the inner membrane is associated with the cleavage of PINK1 from 64-kDa into a 60-kDa form. PINK1 is then cleaved by
PARL into a 52-kDa form. This new form of PINK1 is degraded by proteases within the mitochondria. This keeps the concentration of PINK1 in check in healthy mitochondria.
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.
It is thought that PINK1 phosphorylates Parkin ubiquitin ligase at S65 which initiates Parkin recruitment at the mitochondria.
[Lazarou M. "Keeping the immune system in check: a role for mitophagy. ''Immunol Cell Biol.'' 2014;] 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. This allows for Parkin-mediated ubiquitination on other proteins.
Because of its PINK1-mediated recruitment to the mitochondrial surface, Parkin can ubiquitylate proteins in the outer mitochondrial membrane. Some of these proteins include
Mfn1/
Mfn2 and
mitoNEET
The CDGSH iron sulfur domain are a group of iron-sulfur (2Fe-2S) clusters and a unique 39 amino acid CDGSH domain ''C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H
The CDGSH iron sulfur domain 1 protein (also referred to as mitoNEET) is an integral m ...
.
The ubiquitylation of mitochondrial surface proteins brings in mitophagy initiating factors. Parkin promotes ubiquitin chain linkages on both K63 and K48. K48 ubiquitination initiates degradation of the proteins, and could allow for passive mitochondrial degradation. K63 ubiquitination is thought to recruit autophagy adaptors LC3/GABARAP which will then lead to mitophagy. It is still unclear which proteins are necessary and sufficient for mitophagy, and how these proteins, once ubiquitylated, initiate mitophagy.
Other pathways that can induce mitophagy includes mitophagy receptors on the outer mitochondrial membrane surface. These receptors include NIX1,
BNIP3 and
FUNDC1
FUN14 domain containing 1 is a protein that in humans is encoded by the FUNDC1 gene.
Model organisms
Model organisms have been used in the study of FUNDC1 function. A conditional knockout mouse line, called ''Fundc1tm1a(KOMP)Wtsi'' was generate ...
. 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
In
neurons
A neuron, neurone, or nerve cell is an electrically excitable cell that communicates with other cells via specialized connections called synapses. The neuron is the main component of nervous tissue in all animals except sponges and placozoa. ...
, mitochondria are distributed unequally throughout the cell to areas where energy demand is high, like at
synapses and
Nodes of Ranvier. This distribution is maintained largely by motor protein-mediated mitochondrial transport along the
axon
An axon (from Greek ἄξων ''áxōn'', axis), or nerve fiber (or nerve fibre: see spelling differences), is a long, slender projection of a nerve cell, or neuron, in vertebrates, that typically conducts electrical impulses known as action ...
. While neuronal mitophagy is thought to occur primarily in the
cell body, it also occurs locally in the axon at sites distant from the cell body; in both the cell body and the axon, neuronal mitophagy occurs via the PINK1-Parkin pathway. Mitophagy in the nervous system may also occur transcellularly, where damaged mitochondria in
retinal ganglion cell
A retinal ganglion cell (RGC) is a type of neuron located near the inner surface (the ganglion cell layer) of the retina of the eye. It receives visual information from photoreceptors via two intermediate neuron types: bipolar cells and reti ...
axons can be passed to neighboring
astrocytes
Astrocytes (from Ancient Greek , , "star" + , , "cavity", "cell"), also known collectively as astroglia, are characteristic star-shaped glial cells in the brain and spinal cord. They perform many functions, including biochemical control of endo ...
for degradation. This process is known as transmitophagy.
In yeast
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.
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.
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.
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.
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.
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
BNIP3-mediated mitophagy, have been associated with tumor suppression in humans and mice. Mitophagy associated with
NIX, in contrast, is associated with tumor promotion. In 1920
Otto Warburg Otto Warburg may refer to:
* Otto Warburg (botanist) (1859–1938), German botanist
* Otto Heinrich Warburg (1883–1970), German physiologist
{{Hndis, Warburg, Otto ...
observed that certain cancerous tumors display a metabolic shift towards
glycolysis. This is referred to as the "
Warburg effect", in which cancer cells produce energy via the conversion of glucose into lactate, even in the presence of oxygen (aerobic glycolysis). Despite nearly a century since it was first described, a lot of questions remained unanswered regarding the Warburg effect. Initially, Warburg attributed this metabolic shift to
mitochondrial dysfunction
Mitochondrial disease is a group of disorders caused by mitochondrial dysfunction. Mitochondria are the organelles that generate energy for the cell and are found in every cell of the human body except red blood cells. They convert the energy of ...
in cancer cells. Further studies in tumor biology have shown that the increased growth rate in cancer cells is due to an overdrive in glycolysis (glycolytic shift), which leads to a decrease in oxidative phosphorylation and mitochondrial density. As a consequence of the Warburg effect, cancer cells would produce large amounts of lactate. The excess lactate is then released to the extracellular environment which results in a decrease in extracellular pH. This micro-environment acidification can lead to cellular stress, which would lead to autophagy. Autophagy is activated in response to a range of stimuli, including nutrient depletion, hypoxia, and activated oncogenes. However, it appears that autophagy can help in cancer cell survival under conditions of metabolic stress and it may confer resistance to anti-cancer therapies such as radiation and chemotherapy. Additionally, in the microenvironment of cancer cells, there is an increase in hypoxia-inducible transcription factor 1-alpha (
HIF1A), which promotes expression of
BNIP3, an essential factor for mitophagy.
Parkinson's disease
Parkinson's disease
Parkinson's disease (PD), or simply Parkinson's, is a long-term degenerative disorder of the central nervous system that mainly affects the motor system. The symptoms usually emerge slowly, and as the disease worsens, non-motor symptoms becom ...
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 and Parkin.
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. Disorders in energy creation by mitochondria can cause cellular degeneration, like those seen in the substantia nigra.
Tuberculosis
Tuberculosis
Tuberculosis (TB) is an infectious disease usually caused by ''Mycobacterium tuberculosis'' (MTB) bacteria. Tuberculosis generally affects the lungs, but it can also affect other parts of the body. Most infections show no symptoms, in w ...
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
References
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Cell biology