Understanding Mitophagy Mechanisms: Canonical PINK1/Parkin, LC3-Dependent Piecemeal, and LC3-Independent Mitochondrial Derived Vesicles

By Christina Towers, PhD

What is Mitophagy?

The selective degradation of mitochondria via double membrane autophagosome vesicles is called mitophagy. Damaged mitochondria can generate harmful amounts of reactive oxygen species (ROS), accumulate damaged mitochondrial DNA, and induce cell death. Mitophagy functions in coordination with mitochondrial biogenesis and changes in mitochondrial dynamics to maintain overall mitochondrial homeostasis.¹ It was generally accepted that the same complexes necessary for the formation of autophagosomes were also important for mitophagy with the potential addition of mitophagy specific adaptor proteins.² But, recent advances in molecular and cellular biology techniques to monitor mitophagy have revealed more complexities indicating distinct forms of mitophagy may take place under specific contexts.³

More than one type of Mitophagy

Canonical mitophagy involves the engulfment of an intact mitochondria into a forming autophagosome. In addition to the general autophagy machinery including LC3 conjugation, this process is largely dependent on PINK1 and Parkin proteins.  After a mitochondrial-targeting insult, PINK1 is stabilized on the outer mitochondria membrane where it then activates the E3 ubiquitin ligase Parkin protein. In an elegant study, five key autophagy receptors were knocked out (KO) to generate penta KO cells that lacked p62/SQSTM1, NBR1, NDP52, OPTN, and TAX1BP1. In add back experiments, it was discovered that OPTN and NDP52 are the two most critical receptors for canonical PINK1/Parkin protein mediated mitophagy. Interestingly, Parkin is not completely necessary for recruitment of receptors and parkin independent mitophagy has also been described.⁴

A second form of mitophagy occurs when a growing autophagosome forms around part of an intact mitochondria that is simultaneously undergoing mitochondrial fission. Small parts of mitochondria can then be recycled in a piecemeal manner.⁵ This process is also dependent on LC3-mediated autophagosome formation as well as mitochondrial fission, although small fragments of mitochondria can still be engulfed in the absence of the mitochondrial fission protein, DRP1.⁶ Piecemeal mitophagy helps maintain homeostasis. Starvation induced autophagy can preferentially promote this form of mitophagy in some contexts⁷, presumably to generate amino acids from the nutrient rich mitochondria without compromising mitochondrial function. However, another study showed that under starvation conditions, Drp1 can be inhibited, resulting on decreased mitochondrial fission and mitophagy in order to protect mitochondrial networks.⁸

A third form of mitochondrial degradation cannot be classified as mitophagy because it does not involve canonical LC3-mediated autophagosomes. Instead, damaged and oxidized mitochondrial proteins are engulfed in small mitochondrial derived vesicles (MDVs) that are shed from intact mitochondria. The vesicles transition through multivesicular bodies before fusing directly with lysosomes in a form of micro-autophagy. Unlike piecemeal mitophagy, mitochondrial fission is dispensable for this process, but similar to canonical mitophagy, Parkin’s E3 ubiquitin ligase activity is necessary.

These three forms of mitochondrial delivery to lysosomes including canonical mitophagy, piecemeal mitophagy, and mitochondrial derived vesicles are likely coordinated. However, the exact cellular contexts that promote one over the other and the crosstalk between all of the mitophagy modalities remains largely unknown.