C53 and Ufmylation Regulation In Endoplasmic Reticulum-Autophagy (ER-phagy)

Project Information

CURIE

Grant agreement ID: 101028611

DOI

10.3030/101028611

Project closed

EC signature date 9 March 2021

Start date 1 May 2021

End date 30 April 2023

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 186 167,04

EU contribution

€ 186 167,04

Coordinated by

GREGOR MENDEL INSTITUT FUR MOLEKULARE PFLANZENBIOLOGIE GMBH
Austria

Periodic Reporting for period 1 - CURIE (C53 and Ufmylation Regulation In Endoplasmic Reticulum-Autophagy (ER-phagy))

Reporting period: 2021-05-01 to 2023-04-30

Summary of the context and overall objectives of the project

Persistent cellular stress impairs cell fitness and lifespan. When stress happens, protein aggregates will be formed, these could be cleared by the essential and fundamental cellular protein quality control pathway called autophagy. Defects in autophagy are linked to diverse diseases in humans and makes plants susceptible to stress.

Endoplasmic reticulum (ER) has a central role for protein biosynthesis, it works together with ribosomes to synthesize, fold and modify lipid and transmembrane proteins. When ER stress happens, cell will initiate an ER-specific autophagic pathway celled “ER-phagy” to remove the damaged ER and maintain a healthy proteome. When ribosomes collide on the ER, another quality control mechanism will be triggered called “UFMylation”, this modification on certain ribosome protein will cooperates with ER-phagy to get rid of incompletely synthesized proteins at the ER-membrane.

The host lab has discovered C53 protein as a conserved ER-phagy receptor from plants to humans. It forms a complex with UFMylation pathway E3 ligase and mediate the UFMylation of ribosome protein, meanwhile bind to autophagy receptor protein ATG8 and mediate ER-phagy. In this project, we dissect how UFMylation regulates C53-mediated ER-phagy, and what is the molecular switch mechanism that regulate the C53 function in normal conditions and under ER-stress.

The project has achieved most of its objectives and milestones for the period, with relatively minor deviations. By the end of this action, together with my colleague, we structurally and genetically characterized C53-ATG8 and C53-UFM1 interaction. Apart from this, using proteomics, I determined the ufmylome in model plant Arabidopsis and established the pipeline for identifying ufmylation substrates in plants. The research carried on during this action expanded our current understanding of a novel ER quality control pathway in plants and our knowledge of ufmylation in plants.

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

Together with colleagues and collaborators, we have characterized the interaction of C53-ATG8 and C53-UFM1 using molecular and biophysics approaches, together with cell biology approaches and plant genetics characterizations, combining with evolutionary analysis. We have uncover the role of UFMylation and the molecular switch that regulates C53 mediated ER-phagy under stress conditions in plants.

Results is published as the cover paper in The EMBO Journal (Volume 42, issue 10, 15 May 2023), titled “Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy”.

Link to the press release of the article on GMI website: https://www.oeaw.ac.at/gmi/detail/news/autophagy-the-molecular-regulation-of-self-eating

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)

One of the most exciting and dynamic fields in protein structure-function study is to look into the functional innovations encoded in intrinsically disordered regions (IDR). At the end of this project, we have mechanistically characterized the evolutionary basis of a novel motif located in an IDR region in C53 protein, and it is critical for regulating a novel ER-phagy. We have demonstrated that the competition between two ubiquitin-like molecules, UFM1 and ATG8 creates a molecular switch in the master regulator C53 in the IDR region, thus initiating ER-phagy.

This mechanism is essential to prevent cells from “eating” healthy cellular components, and this mechanism is conserved across different species, these findings will be of interest to broader scientific audiences working on proteinstasis, autophagy, ER-stress, and also to evolutionary biologists.

Further, as fungi and some eukaryotic parasites have lost the UFMylation pathway at a more recent time in evolution, these organisms must have evolved analogous mechanisms to maintain the ER homeostasis. Thus, identifying such mechanisms in fungi, but also in parasites affecting plants, animals, and even humans would open up potential translational avenues for discover new drugs, which could have potential social-economic impact and suggests a wider social implication.

The cover image highlight our article published in The EMBO Journal on this project