Endoplasmic reticulum remodelling via ER-phagy pathways

Project Information

ER-REMODEL

Grant agreement ID: 101055213

DOI

10.3030/101055213

EC signature date 22 July 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 496 691,25

EU contribution

€ 2 496 691,00

Coordinated by

JOHANN WOLFGANG GOETHE-UNIVERSITAET FRANKFURT AM MAIN
Germany

Periodic Reporting for period 1 - ER-REMODEL (Endoplasmic reticulum remodelling via ER-phagy pathways)

Reporting period: 2023-01-01 to 2025-06-30

Summary of the context and overall objectives of the project

The project ER-REMODEL aims to explore the structural changes that undergo the endoplasmic reticulum (ER), a key organelle responsible for protein and lipid synthesis. The structural remodelling of the ER membrane is primarily driven by ER-phagy, a process that ensures cellular homeostasis by selectively degrading portions of the ER. Therefore, ER-REMODEL focuses on ER-phagy receptors, which facilitate the connection between ER membranes and the autophagic machinery. Although ER-phagy receptors are known, the molecular mechanisms regulating ER-phagy and ER remodelling remain poorly understood. In this regard, ER-REMODEL aims to uncover how site-specific ubiquitination and receptor clustering control ER-phagy, impacting ER dynamics in different cell types and under stress conditions.

ER-REMODEL has four main objectives:
1. Understanding the mechanisms of ER remodelling via ER-phagy.
2. Deciphering the structural and biophysical properties of ER-phagy receptors.
3. Using computational modelling to simulate and predict molecular events in ER-phagy.
4. Investigating the role of ER-phagy in disease, including neuropathies and bacterial infections.

ER-REMODEL is bringing novel and ground-breaking discoveries to elucidate an “ER-phagy receptor code” controlling ER remodelling in health and disease linked to ER dysfunction, such as neurodegenerative disorders and infections. Moreover, ER-REMODEL is establishing a broader conceptual framework for future studies into the dynamic regulation of other cellular organelles via ubiquitin-driven selective autophagy.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first two years of the project ER-REMODEL, we made significant progress in understanding how ubiquitination regulates ER membrane remodelling. The project has already resulted in several high-impact research publications and key discoveries in each of its objectives:
1. Ubiquitination of the ER-phagy receptor FAM134B by the ligase AMFR enhances its clustering, facilitating the degradation of portions of the ER.
2. The protocols for purifying the FAM134B reticulon homology domain were established, allowing the study of its oligomeric assembly.
3. Computational modelling revealed that FAM134B clustering enhances membrane curvature. The predictions were confirmed experimentally.
4. FAM134B and ARL6IP1 interaction forms heteromeric complexes crucial for ER remodelling. Loss of ARL6IP1 in mice leads to expanded ER sheets, impaired ER-phagy and progressive neuronal degeneration.
Beyond biological discoveries, ER-REMODEL contributes to developing technological approaches to studying ER-phagy. These approaches include: mass spectrometry-based mapping of ubiquitination sites, bimolecular complementation affinity purification assay and DNA-PAINT microscopy.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In its first two years, the project ER-REMODEL has made significant advances that go beyond the current state-of-the-art by revealing previously unknown molecular mechanisms of ER-phagy and its connection to neurodegenerative diseases. Indeed, one of the most groundbreaking discoveries was that ubiquitination stabilises and enhances the clustering of FAM134B, promoting the formation of ER-phagy initiation sites and facilitating ER membrane remodelling. The project used computational modelling to demonstrate how these ubiquitinated clusters induce sharp membrane curvature, leading to selective ER fragmentation for degradation. The project brought a level of mechanistic detail that had not been achieved thus far. Moreover, identifying ARL6IP1 as a key partner in ER-phagy, and its link to neurodegenerative pathologies, provides a new molecular framework for understanding the role of ER remodelling in neurodegeneration.