IPA reshapes the autophagy cargo hierarchy by biasing p62 toward mitochondrial ROS sensing

Aaliya Owusu· Mar 21, 2026

Mechanism: Gut metabolite IPA reduces mitochondrial ROS, shifting the p62 protein's cargo preference to target damaged mitochondria for degradation. Readout: Readout: This results in increased mitophagy and decreased ER stress, alongside altered p62 oligomerization and LC3-II/I ratios in specific cellular compartments.

Hypothesis

Indole-3-propionic acid (IPA) produced by gut microbiota directly modulates the selectivity of p62/SQSTM1–mediated autophagy by altering its redox sensing, thereby shifting the degradation hierarchy toward mitochondria and away from the endoplasmic reticulum under nutrient stress.

Mechanistic rationale

IPA is a potent antioxidant that can scavenge mitochondrial superoxide and modulate intracellular ROS levels ().
p62 contains cysteine residues that form disulfide bonds in response to ROS, influencing its oligomerization and ubiquitin chain preference ().
Elevated ROS promotes p62 binding to K63-linked ubiquitin on damaged mitochondria, favoring mitophagy, whereas low ROS shifts p62 toward K48-linked substrates and ER-associated cargo ().
Therefore, microbiota‑derived IPA, by buffering mitochondrial ROS, would bias p62 toward a state that preferentially engages mitochondrial cargo, reinforcing the mitophagy arm of the autophagy hierarchy.

Testable predictions

In vitro: Treating HEK293 cells with physiological concentrations of IPA (10‑50 µM) will increase p62 oligomerization (detected by non‑reducing SDS‑PAGE) and enhance colocalization of p62 with mitochondrial markers (TOM20) after CCCP treatment, while decreasing p62‑ER colocalization (calnexin) under tunicamycin stress.
In vivo: Old mice (24 mo) receiving IPA in drinking water (5 mM) for 8 weeks will show a higher LC3‑II/I ratio in mitochondrial fractions and a lower ratio in ER fractions compared with age‑matched controls, accompanied by reduced mitochondrial ROS (MitoSOX) and ER stress markers (CHOP, BiP).
Genetic specificity: The effect of IPA will be abolished in p62‑Cys‑to‑Ser mutants that cannot sense ROS, confirming that IPA acts through p62 redox sensing rather than bulk autophagy induction.
Pharmacological control: Co‑administration of the ROS‑sensitizer SQ‑1 will not further increase mitophagy beyond IPA alone, indicating that both compounds converge on the same p62‑ROS node.

Falsifiability

If IPA fails to alter p62 oligomerization or does not shift the mitochondrial/ER autophagy balance in the assays above, the hypothesis is refuted. Likewise, if p62 redox‑dead mutants still respond to IPA with altered selectivity, the proposed mechanism is incorrect.

Implications

Confirming that a gut‑derived metabolite can reprogram the autophagy cargo hierarchy would link microbiome health directly to selective organelle quality control, offering a mechanistic explanation for IPA’s association with biological age and opening a route to intervene in age‑related decline by tuning autophagy’s triage logic.

Mechanistic rationale

IPA is a potent antioxidant that can scavenge mitochondrial superoxide and modulate intracellular ROS levels ().

p62 contains cysteine residues that form disulfide bonds in response to ROS, influencing its oligomerization and ubiquitin chain preference ().

Elevated ROS promotes p62 binding to K63-linked ubiquitin on damaged mitochondria, favoring mitophagy, whereas low ROS shifts p62 toward K48-linked substrates and ER-associated cargo ().

Therefore, microbiota‑derived IPA, by buffering mitochondrial ROS, would bias p62 toward a state that preferentially engages mitochondrial cargo, reinforcing the mitophagy arm of the autophagy hierarchy.

Testable predictions

In vitro: Treating HEK293 cells with physiological concentrations of IPA (10‑50 µM) will increase p62 oligomerization (detected by non‑reducing SDS‑PAGE) and enhance colocalization of p62 with mitochondrial markers (TOM20) after CCCP treatment, while decreasing p62‑ER colocalization (calnexin) under tunicamycin stress.

In vivo: Old mice (24 mo) receiving IPA in drinking water (5 mM) for 8 weeks will show a higher LC3‑II/I ratio in mitochondrial fractions and a lower ratio in ER fractions compared with age‑matched controls, accompanied by reduced mitochondrial ROS (MitoSOX) and ER stress markers (CHOP, BiP).

Genetic specificity: The effect of IPA will be abolished in p62‑Cys‑to‑Ser mutants that cannot sense ROS, confirming that IPA acts through p62 redox sensing rather than bulk autophagy induction.

Pharmacological control: Co‑administration of the ROS‑sensitizer SQ‑1 will not further increase mitophagy beyond IPA alone, indicating that both compounds converge on the same p62‑ROS node.

Implications