
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.28.609967
preprint
1
Article
Reconstitution of BNIP3/NIX-mediated autophagy reveals two pathways and hierarchical flexibility of the initiation machinery
Adriaenssens Elias http://orcid.org/0000-0001-9430-917X

Schaar Stefan http://orcid.org/0009-0009-6733-7277

Cook Annan S.I. http://orcid.org/0000-0001-6415-9107

Stuke Jan F. M. http://orcid.org/0009-0007-5583-4941

Sawa-Makarska Justyna http://orcid.org/0000-0002-9321-976X

Nguyen Thanh Ngoc http://orcid.org/0000-0001-9698-0020

Ren Xuefeng http://orcid.org/0000-0002-4822-4316

Schuschnig Martina
Romanov Julia http://orcid.org/0000-0002-2875-9487

Khuu Grace http://orcid.org/0000-0002-2550-0605

Lazarou Michael http://orcid.org/0000-0003-2150-5545

Hummer Gerhard http://orcid.org/0000-0001-7768-746X

Hurley James H. http://orcid.org/0000-0001-5054-5445

Martens Sascha http://orcid.org/0000-0003-3786-8199

28 8 2024
2024.08.28.609967https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://biorxiv.org/lookup/doi/10.1101/2024.08.28.609967
nihpp-2024.08.28.609967.pdf
SUMMARY

Selective autophagy is a lysosomal degradation pathway that is critical for maintaining cellular homeostasis by disposing of harmful cellular material. While the mechanisms by which soluble cargo receptors recruit the autophagy machinery are becoming increasingly clear, the principles governing how organelle-localized transmembrane cargo receptors initiate selective autophagy remain poorly understood. Here, we demonstrate that transmembrane cargo receptors can initiate autophagosome biogenesis not only by recruiting the upstream FIP200/ULK1 complex but also via a WIPI-ATG13 complex. This latter pathway is employed by the BNIP3/NIX receptors to trigger mitophagy. Additionally, other transmembrane mitophagy receptors, including FUNDC1 and BCL2L13, exclusively use the FIP200/ULK1 complex, while FKBP8 and the ER-phagy receptor TEX264 are capable of utilizing both pathways to initiate autophagy. Our study defines the molecular rules for initiation by transmembrane cargo receptors, revealing remarkable flexibility in the assembly and activation of the autophagy machinery, with significant implications for therapeutic interventions.
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