Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns

Abstract

Macroautophagy (henceforth autophagy) an evolutionary conserved intracellular pathway, involves lysosomal degradation of damaged and superfluous cytosolic contents to maintain cellular homeostasis. While autophagy was initially perceived as a bulk degradation process, a surfeit of studies in the last 2 decades has revealed that it can also be selective in choosing intracellular constituents for degradation. In addition to the core autophagy machinery, these selective autophagy pathways comprise of distinct molecular players that are involved in the capture of specific cargoes. The diverse organelles that are degraded by selective autophagy pathways are endoplasmic reticulum (ERphagy), lysosomes (lysophagy), mitochondria (mitophagy), Golgi apparatus (Golgiphagy), peroxisomes (pexophagy) and nucleus (nucleophagy). Among these, the main focus of this review is on the selective autophagic pathway involved in mitochondrial turnover called mitophagy. The mitophagy pathway encompasses diverse mechanisms involving a complex interplay of a multitude of proteins that confers the selective recognition of damaged mitochondria and their targeting to degradation via autophagy. Mitophagy is triggered by cues that signal the mitochondrial damage such as disturbances in mitochondrial fission-fusion dynamics, mitochondrial membrane depolarisation, enhanced ROS production, mtDNA damage as well as developmental cues such as erythrocyte maturation, removal of paternal mitochondria, cardiomyocyte maturation and somatic cell reprogramming. As research on the mechanistic aspects of this complex pathway is progressing, emerging roles of new players such as the NIPSNAP proteins, Miro proteins and ER-Mitochondria contact sites (ERMES) are being explored. Although diverse aspects of this pathway are being investigated in depth, several outstanding questions such as distinct molecular players of basal mitophagy, selective dominance of a particular mitophagy adapter protein over the other in a given physiological condition, molecular mechanism of how specific disease mutations affect this pathway remain to be addressed. In this review, we aim to give an overview with special emphasis on molecular and signalling pathways of mitophagy and its dysregulation in neurodegenerative disorders.

Keywords: mitochondrial dynamics; mitochondrial dysfunction; mitophagy; neurodegenaration; phosphorylation; ubiquitination.

FIGURE 1

Mitochondrial fission-fusion dynamics and mitophagy. A healthy mitochondrion is endowed with proteins on its outer membrane such as SNPH, MYO19, dynein-dynactin complex, MIRO-TRAK complex, kinesins, which enable efficient trafficking of the organelle on cytoskeletal tracks. Onset of mitochondrial damage initiates constriction of mitochondrial membrane, wherein ER tightens around the mitochondrial filament mediated by IFN2, mitoSpire1C and NMIIA induced actin polymerisation. This pre-constriction step results in the recruitment of DRP1 onto the mitochondrial membrane. A burst of actin polymerisation around the damaged mitochondria is enhanced, resulting in its fragmentation from the healthy pool. Mitochondrial damage also leads to the localisation of PINK1-Parkin complex onto OMM, initiating a feed forward loop leading to proteasomal degradation of many OMM proteins such as MIRO proteins and MFN2. Degradation of these proteins results in the detachment of motor proteins and ER tethers. This process arrests trafficking of damaged mitochondria and also increases their distance from ER. Additionally, it also prevents the fusion of damaged mitochondria to the healthy pool. Actin filamentation now completely cages the damaged mitochondria, recruiting MYO6 which interacts with both ubiquitin and autophagy adaptor proteins. This whole cascade of events facilitates the engulfment of damaged mitochondria by autophagic machinery resulting in the formation of a mitophagosome which would eventually fuse with lysosome.

FIGURE 2

Mitophagy pathway. (A) Recruitment of mitophagy related proteins on OMM. On mitochondrial insult, the damaged part of the mitochondrial network undergoes autophagy mediated degradation. A damaged mitochondria recruits several proteins on their surface that interact with the autophagy machinery in receptor dependent or PINK1-Parkin dependent manner. Hypoxia induces recruitment of BNIP3 which upon phosphorylation at its Ser17 and Ser24 interacts with Atg8 family of proteins. Nix interacts with LC3 upon phosphorylation at its Ser34 and Ser35 positions. FUNDC1 interacts with the autophagy proteins and this is regulated by phosphorylation events at Ser13 by CK2 and Tyr18 by Src kinase. FKBP8 selectively interacts with LC3A. Mitochondrial damage results in phosphorylation of cardiolipin, that translocates from IMM to OMM and then interacts with autophagic machinery. AMBRA1 acts as a mitophagy receptor and is regulated by IKKα mediated phosphorylation. In yeast, binding of mitophagy receptor Atg32 with Atg11 and Atg8 is governed by phosphorylation at its Ser114 and Ser119 residues. Initial phosphorylation of Parkin by PINK1 at Ser65 in its ubiquitin domain triggers a feedforward loop recruiting more Parkin onto OMM. Parkin then ubiquitinates various OMM proteins such as MFN2, VDAC and Miro. This phosphorylation-ubiquitination mediated feed-forward loop amplifies the recruitment of different autophagy adaptor proteins such as NDP52 and OPTN. The phosphorylation of OPTN and NDP52 is mediated by TBK1. NIPSNAP proteins accumulate on the damaged mitochondria in a PINK1-Parkin dependent manner and recruit downstream autophagy proteins, promoting mitophagy. (B) Mitophagosome expansion and closure. Recruitment of mitophagy related proteins on OMM initiates an interaction of the proteins with components of autophagic machinery. The autophagosome then expands around the damaged mitochondria, engulfing them. This expansion is regulated by MONZ1-CCZ1 Rab GEF mediated Rab5 and Rab7 cycles. Phosphorylation Rab7 by TBK1 enhances its interaction with Atg9 vesicles. Mitochondrial GAPs, TBC1D15 and TBC1D17 functions downstream of Parkin and work in concert with FIS1 and LC3 to recruit Rab7 onto the mitochondrial surface shaping mitophagosome. Atg9 and Rab cycles mediate expansion of mitophagosome. Subsequently, the closure of mitophagosome is mediated by the ESCRT complex. Completely sealed mitophagosome then fuses with the lysosome facilitated by fusion proteins such as, PLEKHM1.

FIGURE 3

Mechanisms of mitophagy dysregulation in neurodegenerative disorders. AD: (A) AD associated mutations in presenilin 2 (mPS2) blocks mitophagosome to lysosome fusion by affecting the Rab7 recruitment, leading to accumulation of mitophagosomes. (B) AD associated mutations in presenilin 1 (mPS1) gene decrease the lysosomal acidification by impairing the transport of V-ATPase thereby blocking the clearance of damaged mitochondria. (C) Pathogenic Tau (mTau) interacts with Parkin with its projection domain, inhibiting the recruitment of Parkin to damaged mitochondria. (D) AD models also show down regulation of mitophagy associated proteins PINK1, BNIP3L/NIX, Bcl2L13, p-ULK1, p-TBK1, FUNDC1, AMBRA1, and MUL1 (The red arrow in the figure represents downregulation). PD: (E) PD associated mutations affect the role of Parkin in two ways. Mutations either block Parkin recruitment to damaged mitochondria or impair the ubiquitination capacity of Parkin, both of which impairs the mitophagy pathway. (F) PD associated mutations in LRRK2 impair mitophagy pathway at different stages. Based on specific mutations, LRRK2 hyperphosphorylates Rab10, which prevents its interaction with OPTN thereby blocking its recruitment to damaged mitochondria. Mutant LRRK2 has been shown to prevent the interaction of Parkin with OMM proteins. Mutant LRRK2 also inhibits Miro1 degradation, an essential step for arrest of damaged mitochondria, further impairing the pathway. (G) PD associated mutations in GBA inhibit recruitment of Parkin, NBR1 and LC3 to the damaged mitochondria. HD: Dysregulation of mitophagy pathway by mutant HTT (mHTT) involves multiple mechanisms. (H) mHTT blocks the recruitment of OPTN, NBR1, CALCOCO2 and p62. (I) mHTT stabilizes the interaction of inactive ULK1 to mTOR, thereby impairing the formation of autophagy initiation complex. mHTT promotes degradation of Beclin1, which also prevents the formation of autophagy initiation complex. ALS: (J) Mutant SOD1 (mSOD1) aggregates sequester OPTN preventing its recruitment to damaged mitochondria. (K) ALS associated mutations in OPTN (mOPTN) blocks its recruitment to damaged mitochondria and also impairs its interaction with myosin VI, thereby restricting the localization of mutant OPTN in cytoplasm. (L) ALS linked mutations in TBK1 (mTBK1) blocks its recruitment to damaged mitochondria, impairs its interaction with OPTN and impedes the recruitment of LC3 to damaged mitochondria. (M) In addition, mitophagy related proteins PINK1, Parkin, p62, and BNIP3 are downregulated in ALS (The red arrow in the figure represents downregulation).