Structural basis for the selective inhibition of the PI3KC3-C2 complex by Rubicon in endolysosome maturation and mitophagy

Verdict. Rubicon is specific for the UVRAG-containing PI3KC3-C2 over the purely autophagic ATG14-containing PI3KC3-C1 complex. It intersects mitochondrial stress/dysfunction themes (mitochondrial dysfunction; mitophagy; OXPHOS / ETC).

What the authors report

Rubicon is a negative regulator of autophagy and the endolysosomal network (ELN) and an antagonist of the class III phosphatidylinositol 3-kinase complex II (PI3KC3-C2). Inhibition of Rubicon is considered a potential means to therapeutically upregulate autophagy and the ELN to treat Parkinsons disease and other conditions characterized by autophagic and ELN dysfunction.

Key results stated in the abstract include the following. Rubicon is specific for the UVRAG-containing PI3KC3-C2 over the purely autophagic ATG14-containing PI3KC3-C1 complex. Here, we determined the high-resolution cryo-electron microscopy structure of PI3KC3-C2 in complex with the PI3KC3-binding domain (PIKBD) of Rubicon and compared it to cryo-EM structures of unbound PI3KC3-C2 and PI3KC3-C1. The selectivity of Rubicon for the PI3KC3-C2 complex over the PI3KC3-C1 complex is attributed to a conformation of the BECN1BARA domain induced by UVRAG, rather than to direct contact with UVRAG or direct antagonism by the ATG14 subunit of PI3KC3-C1.

Why it matters for mitochondrial biology

Within mitochondrial research, this work maps primarily to mitophagy, OXPHOS, redox biology, neurobiology. It is relevant to mitochondrial dysfunction discourse because the abstract invokes mitochondrial dysfunction, mitophagy, OXPHOS / ETC, disease context. That does not by itself establish a validated disease mechanism; it indicates thematic proximity. Because a therapeutic or interventional angle is present, the piece is of interest for mitochondrial-targeted drug hypothesis generation—subject to full-text validation of endpoints and safety context. OXPHOS/ETC involvement, if confirmed, would place the work in the core of bioenergetic pathophysiology rather than peripheral organelle biology. Server: biorxiv. Posted 2026-08-10. Synthesis confidence is bounded by abstract completeness.

Study design (abstract-level)

Targeted disruption of the Rubicon:PI3K3-C2 structural interface by site-directed mutations enhances mitophagic activity in human epithelial cells to levels comparable to those observed in Rubicon knockout (KO) cells.

Principal findings

1. Rubicon is specific for the UVRAG-containing PI3KC3-C2 over the purely autophagic ATG14-containing PI3KC3-C1 complex.
2. Here, we determined the high-resolution cryo-electron microscopy structure of PI3KC3-C2 in complex with the PI3KC3-binding domain (PIKBD) of Rubicon and compared it to cryo-EM structures of unbound PI3KC3-C2 and PI3KC3-C1.
3. The selectivity of Rubicon for the PI3KC3-C2 complex over the PI3KC3-C1 complex is attributed to a conformation of the BECN1BARA domain induced by UVRAG, rather than to direct contact with UVRAG or direct antagonism by the ATG14 subunit of PI3KC3-C1.
4. Similarly, disruption of the interaction in Rubicon-overexpressing hippocampal neurons restored lysosomal flux to wild-type levels.
5. These data show that suppressing the function of PI3K3-C2 can fully account for the negative regulatory effects of Rubicon in the autophagy and ELN pathways.

Limitations of this brief

• This Mitos brief is an abstract-level synthesis of a preprint; it is not peer review and not a substitute for reading the full paper.
• Preprint status: findings may change with revision or journal review.
• Effect sizes, n numbers, statistics, and full experimental controls are typically incomplete at abstract resolution.
• Primary source: biorxiv DOI 10.64898/2026.08.07.743589 (posted 2026-08-10).

Open scientific questions

• Which specific experimental panels in the full paper establish the strongest causal claim, and how robust are the controls?
• Are OXPHOS defects primary drivers or secondary consequences of broader cellular stress?
• What dose, timing, and off-target profile would be required to take the intervention seriously as a therapeutic hypothesis?
• Does the work distinguish mitophagy flux from static marker changes (e.g., LC3, PINK1/Parkin pathway activity)?
• Is the mitochondrial phenotype cell-autonomous in neurons/glia, or secondary to systemic/inflammatory signals?

Bottom line

For mitochondrial biologists focused on mitophagy, OXPHOS, redox biology, this preprint is worth full-text review if the topic matches your program. Abstract-level takeaway: Rubicon is specific for the UVRAG-containing PI3KC3-C2 over the purely autophagic ATG14-containing PI3KC3-C1 complex. Confirm methods, effect sizes, and controls in the full PDF before citing the result as established.

Bibliographic record

Abstract-based editorial synthesis by Mitos. Not peer review.