Localacetyl-CoA gradients at organelles set the hierarchy of selective autophagy, and their age‑dependent dysregulation rewires cargo prioritization

Hypothesis

The order in which selective autophagy receptors (SARs) engage their cargo is not fixed by receptor abundance alone; instead, it is tuned by micro‑domains of acetyl‑CoA that accumulate at the surface of mitochondria, ER, lysosomes, and peroxisomes. High local acetyl‑CoA acetylates lysine residues on SARs or their adaptor proteins, altering binding affinity for ubiquitin tags and thereby shifting the pecking order of organelle turnover. With age, declining mitochondrial output and altered nucleocytoplasmic transport reduce acetyl‑CoA synthesis at specific organelles, flattening the gradient and causing a mis‑prioritization that leads to selective accumulation of damaged cargoes (e.g., depolarized mitochondria in neurons, ER stress in hepatocytes). This model predicts that restoring organelle‑specific acetyl‑CoA levels will rescue selective autophagy flux without changing global autophagy rates.

Mechanistic Basis

1. Acetyl‑CoA as a post‑translational modifier – Acetyl‑CoA can donate acetyl groups to lysine residues via non‑enzymatic acetylation or via acetyltransferases that are recruited to organelles (e.g., ATAT1 at mitochondria). Acetylation of SARs such as FAM134B (ER‑phagy) or BNIP3 (mitophagy) has been shown to modulate their interaction with LC3 and ubiquitin chains (local acetyl-CoA blocks ER‑phagy).
2. Spatial compartmentalization – Mitochondrial citrate exported via SLC25A1 and cleaved by ACLY generates a cytosolic acetyl‑CoA pool that can be further channeled into organelles by ACSS2 or AT‑1. Nucleocytoplasmic shuttling of acetyl‑CoA carriers (e.g., SLC33A1) creates organelle‑specific microdomains whose size correlates with metabolic activity (nuclear acetyl-CoA regulates TFEB).
3. Age‑related gradient erosion – Aging diminishes NAD+, lowering SIRT3 activity and increasing mitochondrial protein acetylation, which impairs citrate export and reduces local acetyl‑CoA synthesis (aging impairs autophagy via NAD+/SIRT). Concurrently, nuclear acetyl‑CoA drops, reducing TFEB‑driven lysosomal biogenesis. The combined effect is a loss of differential acetyl‑CoA signaling across organelles.
4. Tissue‑specific vulnerability – Organs with high reliance on one organelle (e.g., heart on mitochondria, liver on ER) exhibit the earliest selectivity defects when their specific acetyl‑CoA pool falls below a threshold, explaining the observed tissue‑specific autophagy decline (tissue-specific autophagy decline).

Predictions & Experimental Design

• Prediction 1: Manipulating acetyl‑CoA levels at a single organelle will shift the selectivity hierarchy without altering LC3‑II turnover or global autophagosome number.
  • Test: Target an acetyl‑CoA synthase (ACSS2) or a citrate lyase (ACLY) to mitochondria using a mito‑targeting sequence in cultured neurons. Measure mitochondrial vs. ER phagocytosis using organelle‑specific Keima reporters and ubiquitin‑proteomics of autophagosome cargos.
• Prediction 2: In aged tissues, restoring organelle‑specific acetyl‑CoA will reduce the accumulation of the corresponding damaged organelle and improve functional readouts (e.g., ATP production, protein secretion).
  • Test: Deliver an AAV encoding a mitochondrially targeted ACLY to aged mice; assess mitophagy flux (mt‑Keima), ROS levels, and cognitive performance versus controls.
• Prediction 3: Artificially elevating acetyl‑CoA at the ER in young cells will accelerate ER‑phagy and sensitize cells to ER stress, demonstrating that the gate can be opened or closed by local acetyl‑CoA.
  • Test: Use an ER‑targeted ACSS2 construct and monitor FAM134B‑LC3 interaction via proximity ligation assay under tunicamycin challenge.

Potential Implications

If validated, this hypothesis reframes autophagy decline as a loss of spatial signaling rather than a simple shortage of autophagic machinery. It suggests therapeutic strategies that target organelle‑specific acetyl‑CoA producers or transporters could re‑establish the proper ‘triage’ order of organelle recycling, delaying age‑related pathology without the risks of globally stimulating autophagy.