Molecular Mechanisms of Autophagy

Two ways to eat your mitochondria

In this study we dissected how the two cargo receptors OPTN and NDP52 mediate the degradation of damaged mitochondria in PINK1/Parkin-driven mitophagy. Surprisingly, we found that OPTN uses a novel mode of mitophagy initiation by recruiting the PI3K via TBK1. This was a collaborative study together with the Lazarou lab in the framework of our ASAP funded mito911 team.

See our publication in Molecular Cell.

The illustration was created by Dorotea Fracchiolla (https://my-art-science.com/)

Cooperation of cargo receptors in selective autophagy

During clearance of misfolded, ubiquitinated proteins these cargoes need be recognized and collected within larger condensates followed by the recruitment of the autophagy machinery to mediate their degradation. Employing a blend of reconstitution experiment and cell biological approaches, we have dissected the interplay and individual contributions of the p62, NBR1 and TAX1BP1 cargo receptors during this process. We found that p62 is the main driver of cargo condensation. NBR1 promotes condensate formation by equipping the p62-NBR1 hetero- oligomeric complex with a high-affinity UBA domain. Additionally, NBR1 recruits TAX1BP1 to the ubiquitin condensates formed by p62. While all three receptors interact with FIP200, TAX1BP1 is the main driver of FIP200 recruitment and thus the autophagic degradation of p62–ubiquitin condensates. In summary, our study defines the roles of all three receptors in the selective autophagy of ubiquitin condensates.

See our publication in Nature Communications

The model was created by Dorotea Fracchiolla (https://my-art-science.com/)

Reconstitution of autophagosome nucleation

To stay healthy, our cells must constantly dispose of harmful material. Autophagy, or self-eating, is an important mechanism to ensure the clearance of bulky material. Such material is enwrapped by cellular membranes to form autophagosomes, the contents of which are then degraded. The formation of autophagosomes is a complicated process involving a large number of factors. How they act together in this process is still enigmatic. We recapitulated the initial steps of autophagosome formation using purified autophagy factors from yeast. This approach elucidated some of the organizational principles of the autophagy machinery during the assembly of autophagosomes.

See our publication in Science.

See also Verena’s fantastic video.

“Reverse engineering” autophagosome biogenesis

Together with colleagues from the University of Berkeley (USA) we have reconstituted the activity of key proteins involved in the growth of autophagosome precursors, a process essential for encapsulating cellular components targeted for degradation and recycling. Our results reveal a previously unknown positive feedback loop and activation mechanism that help explain how the autophagy machinery rapidly generates the autophagosomal membrane. The study is published in the Journal of Cell Biology.

Watch Dorotea's amazing animation: https://www.youtube.com/watch?v=soWx_tuJm_g

The Claw grabs the waste

We show that the C-terminal domain of FIP200 binds to the p62 cargo receptor promoting the recruitment and activation of the autophagy machinery at ubiquitin condensates. This in turn results in their sequestration within autophagosomes and eventually degradation of the condensates. Structural studies showed that the C-terminal domain of FIP200 is shaped like a claw. This study is published in Molecular Cell.

Captured by filaments

We found that in vitro the autophagy receptor p62 and ubiquitinated substrates spontaneously phase separate into clusters. Mechanistically, this is based on the crosslinking of p62 filaments by the substrates. We further uncover multiple modes of regulation of the clustering reaction that suggest how this process can be integrated into general proteostasis. This study is published in the EMBO Journal.

The cargo as conductor

We discovered that the yeast cargo receptor Atg19 directly interacts with the E3-like Atg12–Atg5-Atg16 complex via its LIR motifs. In a fully reconstituted system we show that these interactions are sufficient to mediate Atg8 conjugation at the cargo. The recruitment of the E3-like complex to cargo may be conserved since we show that also human cargo receptors bind the ATG5 protein. This study is published in eLife.

Autophagy goes exclusive

We show that the Atg19 cargo receptor contains multiple interaction sites for the Atg8 protein. Atg8 proteins decorate the autophagosomal membrane and collectively these multiple interaction sites for Atg8 bend the membrane around autophagic cargo material. The close apposition of the membrane and the cargo excludes non-cargo material from its delivery into the lysosomal system. This study is published in Nature Cell Biology.