Regulation of autophagy and mitophagy by nutrient availability and acetylation

Abstract

Normal cellular function is dependent on a number of highly regulated homeostatic mechanisms, which act in concert to maintain conditions suitable for life. During periods of nutritional deficit, cells initiate a number of recycling programs which break down complex intracellular structures, thus allowing them to utilize the energy stored within. These recycling systems, broadly named "autophagy", enable the cell to maintain the flow of nutritional substrates until they can be replenished from external sources. Recent research has shown that a number of regulatory components of the autophagy program are controlled by lysine acetylation. Lysine acetylation is a reversible post-translational modification that can alter the activity of enzymes in a number of cellular compartments. Strikingly, the main substrate for this modification is a product of cellular energy metabolism: acetyl-CoA. This suggests a direct and intricate link between fuel metabolites and the systems which regulate nutritional homeostasis. In this review, we examine how acetylation regulates the systems that control cellular autophagy, and how global protein acetylation status may act as a trigger for recycling of cellular components in a nutrient-dependent fashion. In particular, we focus on how acetylation may control the degradation and turnover of mitochondria, the major source of fuel-derived acetyl-CoA.

Keywords: Acetylation; Autophagy; GCN5L1; Mitophagy; Sirt3.

Fig 1

Nutrient depletion pathways in the activation of autophagy. A. In the presence of nutrients, growth factor and amino acids, Sirt1 and AMPK are inactive, whereas AKT is activated by the growth factor receptors. AKT activates mTOR directly, and indirectly by blocking its inhibitor TSC1/2. The mTOR complex sequesters and phosphorylates the Ulk1 complex, and phosphorylates and inhibits the Beclin/class III PI3K complex. P300 acetylates and inhibits LC3, Atg7, Atg5 and ATg12, members of the ubiquitin-like systems involved in the elongation of the phagophore. Autophagy is inhibited. B. In the absence of nutrients, growth factors and amino acids AKT is inactive, whereas AMPK is activated by the low AMP/ATP ratio. AMPK inhibits mTOR directly and indirectly, by activating its inhibitor TSC1/2. AMPK also bind to the Ulk1 complex, phosphorylating Ulk1. The Ulk1 complex phosphorylates the Beclin/class III PI3K complex, which generates PIP3 and this leads to the initiation of the phagophore. Caloric restriction also activates Sirt1, which deacetylates LC3, Atg7, Atg5 and FoXO3. This leads to the activation of the ubiquitin-like systems (Atg5, 12, 16 and LC3-II) involved in the elongation of the phagophore and also to the activation of transcription by FoxO3. The combination of these programs activates cellular autophagy.

Fig 2

Multiple mechanisms are employed in the degradation of mitochondria through mitophagy. Pink1 protein levels are stabilized in depolarized mitochondria, following a reduction in its proteolytic processing by PARL, which triggers the activation of the E3 ubiquitin ligase, Parkin. Parkin ubiquitinylates mitochondrial membrane proteins, which concurrently blocks mitochondria fusion (via the degradation of mitofusin proteins) and directs depolarized organelles to autophagosomes, mediated by p62 and LC3-II. Both hypoxia and cellular differentiation induce mitophagy via NIX and BNIP3, which homo-dimerize and directly bind to LC3-II during autophagosome formation. This dimerization is also thought to free Beclin1 from its interaction with anti-apoptotic BCL-2 family proteins. Hypoxia has also been shown to block FUNDC1 phosphorylation, which results in FUNDC1 binding to LC3-II. Finally, the mitochondria-localized E3 ligase RNF185 ubiquitinylates BNIP3, leading to the targeting of mitochondria to autophagosomes via p62 and LC3-II. (B-cell lymphoma 2, BCL-2; BCL2/adenovirus E1B 19 kDa protein-interacting protein 1/3, BNIP1/3; ring finger protein 185, RNF185; nucleoporin 62, p62; PTEN-induced putative kinase 1, Pink1; voltage dependent anion channel, VDAC; mitofusin, MFN; Presenilins-associated rhomboid-like protein, PARL).

Fig 3

A schematic model of the role of mitochondrial deacetylation in the modulation of selective mitophagy. Fasting or caloric restriction result in the deacetylation of mitochondrial proteins via activation of Sirt3 and the downregulation of GCN5L1. Through an unknown signaling mechanism, perhaps by the direct ubiquitinylation of mitochondrial proteins or via retrograde signaling, mitophagy is initiated. In turn, lysosomal biogenesis in upregulated via the lysosome biogenesis transcription factor EB (TFEB), which is countered be reciprocal upregulation of the mitochondrial biogenesis master regulator peroxisome-proliferator activated receptor gamma, coactivator 1 alpha (PGC-1α). Together these pathways drive mitophagy, mitochondrial turnover and mitochondrial replacement via the mitochondrial biogenesis program.