Autophagosome content profiling reveals receptor-specific cargo candidates

Area of Science:

• Cell Biology
• Molecular Biology
• Autophagy Research

Background:

• Selective autophagy receptors (e.g., SQSTM1/p62, NBR1, CALCOCO2/NDP52, OPTN, TAX1BP1, TOLLIP) mediate the degradation of cellular components.
• The specific protein cargo recognized and degraded by these receptors remains largely unknown.

Purpose of the Study:

• To comprehensively map the protein inventory of autophagosomes associated with six key selective autophagy receptors.
• To identify novel autophagy substrates under basal and stress conditions in mammalian cells.

Main Methods:

• Utilized limited proteolysis-enhanced proximity biotinylation coupled with organelle enrichment.
• Employed quantitative proteomics to analyze autophagosome cargo.
• Investigated cargo under both basal and proteostasis-challenged conditions.

Main Results:

• Identified a diverse range of previously unknown autophagy substrates.
• Discovered that some substrates are degraded via endosomal microautophagy, independent of canonical autophagy pathways.
• Demonstrated distinct degradation routes for substrates dependent on TOLLIP and SQSTM1/p62.

Conclusions:

• This study provides a detailed inventory of autophagosome cargo for multiple selective autophagy receptors.
• Reveals the existence of non-canonical degradation pathways, including endosomal microautophagy, for specific protein substrates.
• Highlights the complexity of cellular protein quality control mechanisms mediated by autophagy.