Role of AMBRA1 in mitophagy regulation: emerging evidence in aging-related diseases

Abstract

Aging is a gradual and irreversible physiological process that significantly increases the risks of developing a variety of pathologies, including neurodegenerative, cardiovascular, metabolic, musculoskeletal, and immune system diseases. Mitochondria are the energy-producing organelles, and their proper functioning is crucial for overall cellular health. Over time, mitochondrial function declines causing an increased release of harmful reactive oxygen species (ROS) and DNA, which leads to oxidative stress, inflammation and cellular damage, common features associated with various age-related pathologies. The impairment of mitophagy, the selective removal of damaged or dysfunctional mitochondria by autophagy, is relevant to the development and progression of age-related diseases. The molecular mechanisms that regulates mitophagy levels in aging remain largely uncharacterized. AMBRA1 is an intrinsically disordered scaffold protein with a unique property of regulating the activity of both proliferation and autophagy core machineries. While the role of AMBRA1 during embryonic development and neoplastic transformation has been extensively investigated, its functions in post-mitotic cells of adult tissues have been limited due to the embryonic lethality caused by AMBRA1 deficiency. Recently, a key role of AMBRA1 in selectively regulating mitophagy in post-mitotic cells has emerged. Here we summarize and discuss these results with the aim of providing a comprehensive view of the mitochondrial roles of AMBRA1, and how defective activity of AMBRA1 has been functionally linked to mitophagy alterations observed in age-related degenerative disorders, including muscular dystrophy/sarcopenia, Parkinson diseases, Alzheimer diseases and age-related macular degeneration.Abbreviations: AD: Alzheimer disease; AMD: age-related macular degeneration; AMBRA1: autophagy and beclin 1 regulator 1; APOE4: apolipoprotein E4; ATAD3A: ATPase family AAA domain containing 3A; ATG: autophagy related; BCL2: BCL2 apoptosis regulator; BH3: BCL2-homology-3; BNIP3L/NIX: BCL2 interacting protein 3 like; CDK: cyclin dependent kinase; CHUK/IKKα: component of inhibitor of nuclear factor kappa B kinase complex; CRL2: CUL2-RING ubiquitin ligase; DDB1: damage specific DNA binding protein 1; ER: endoplasmic reticulum; FOXO: forkhead box O; FUNDC1: FUN14 domain containing 1; GBA/β-glucocerebrosidase: glucosylceramidase beta; HUWE1: HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1; IDR: intrinsically disordered region; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; MCL1: MCL1 apoptosis regulator, BCL2 family member; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; MSA: multiple system atrophy; MYC: MYC proto-oncogene, bHLH transcription factor; NUMA1: nuclear mitotic apparatus protein 1; OMM; mitochondria outer membrane; PD: Parkinson disease; PHB2: prohibitin 2; PINK1: PTEN induced kinase 1; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PTK2/FAK: protein tyrosine kinase 2; ROS: reactive oxygen species; RPE: retinal pigment epithelium; SAD: sporadic AD; SOCS3: suppressor of cytokine signaling 3; SRC, SRC proto-oncogene, non-receptor tyrosine kinase; STAT3: signal transducer and activator of transcription 3; STING1: stimulator of interferon response cGAMP interactor 1; SQSTM1/p62: sequestosome 1; TBK1: TANK binding kinase 1; TGFB/TGFβ: transforming growth factor beta; TOMM: translocase of outer mitochondrial membrane; TRAF6: TNF receptor associated factor 6; TRIM32: tripartite motif containing 32; ULK1: unc-51 like autophagy activating kinase 1.

Keywords: AMBRA1; Aging; aging-related diseases; autophagy; mitochondria; mitophagy.

Figure 1.

Structure of the AMBRA1 protein. (A) Description of structural domains of AMBRA1 proteins. IDR: Intrinsically disorder region. (B) Organization of WD40 domains in AMBRA1 proteins to form a β-barrel structure. (C) Prediction of AMBRA1 structure by alpha fold software. Structural model was obtained from the Alpha fold protein structure database developed by EMBL-EBI and DeepMind (https://alphafold.ebi.ac.uk/entry/Q9C0C7) [142,143]. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation. Color scale Model Confidence: Dark Blue: Very high (pLDDT > 90), Light Blue: Confident (90 > pLDDT > 70), Yellow: Low (70 > pLDDT > 50). Orange: Very low (pLDDT < 50). https://alphafold.ebi.ac.uk/entry/Q9C0C7. The figure was created with BioRender.com.

Figure 2.

Role of AMBRA1 in the regulation of autophagy. Description of the role of AMBRA1 in the regulation of ULK1 complex (ULK1, ATG13, ATG101 and RB1CC1) and BECN1 complex (BECN1, ATG14, PIK3C3/VPS34 and PIK3R4/VPS15) activity by regulative ubiquitination (ULK1 dimer not shown). To promote autophagy, AMBRA1 is recruited to lipid rafts present at the ER-mitochondria contact sites by interacting with ERLIN1. AMBRA1 mediates the non-degradative K63-linked polyubiquitination of ULK1 by the interaction with the ubiquitin ligases TRAF6 and TRIM32. Moreover, AMBRA1 is required for BECN1-PIK3C3/VPS34 complex stability via K63-linked polyubiquitination of BECN1, mediated by the interaction of AMBRA1 with the ubiquitin ligase CRL4 and TRAF6. The bottom panel reports different proteins that are responsible for the repressing AMBRA1 autophagic activity in unstressed conditions. PtdIns3P, phosphatidylinositol-3-phosphate. The figure was created with BioRender.com.

Figure 3.

Role of AMBRA1 in the regulation of mitophagy. Description of the role of AMBRA1 in the regulation of both PINK1-PRKN-dependent and -independent mitophagy. Upper part of the figure: AMBRA1 is required for the accumulation of PINK1 on the OMM following mitochondrial membrane depolarization by interacting with ATAD3A and the TOMM complex. Moreover, AMBRA1 interacts with PRKN to recruit the BECN1-PIK3C3/VPS34 complex and promote autophagosome formation in proximity to damaged mitochondria. Lower part of the figure: AMBRA1 inhibits mitochondria fusion by mediating the degradative degradation of MFN2 by the ubiquitin ligase HUWE1. Moreover, AMBRA1 acts as a mitophagy cargo receptor by interacting with LC3-II on the OMM. This interaction is stimulated by AMBRA1 phosphorylation mediated by CHUK/IKKα. Mitophagic activity of AMBRA1 is inhibited by BCL2 family members. The figure was created with BioRender.com.

Figure 4.

Role of AMBRA1 in the regulation of mitophagy in aging-related degenerative disorders. Description of the role of AMBRA1 in the regulation of mitophagy in age-relate degenerative diseases. Upper panel: decreased AMBRA1 levels in neuronal cells overexpressing GBA^L444P mutant and brain tissues from GBA-PD patients and GBA^L444P heterozygous mice. MIR103A-3p, inhibits AMBRA1 expression levels, as well as PINK1 and PRKN expression, in pharmacologically-induced cellular and mouse models of PD. AMBRA1 associates with SNCA/α-synuclein and this interaction is increased by the phosphorylation of SNCA/α-synuclein observed in Lewy bodies. Right panel: AMBRA1 expression was observed to decrease in cellular and mouse models of Alzheimer disease expressing pathogenic APP mutant or APOE4. Decreased AMBRA1 is associated to a reduction of mitophagy. Left panel: defects in the retinal pigment epithelium (RPE) were observed in heterozygous ambra1 mice showing a reduction in mitochondrial membrane potential, accumulation of protein aggregates, increased neuroinflammation and an impaired antioxidant response, triggering age-related vision loss. Lower panel: AMBRA1 is an important factor regulating both muscle homeostasis and muscle atrophy. AMBRA1 interacts with the ubiquitin ligase TRIM32, promoting the regulative K63-linked polyubiquitination of ULK1 and the induction of mitophagy in muscle cells. The figure was created with BioRender.com.