Richard Vierstra - Autophagy, the master of bulk and selective recycling

Autophagy-mediated turnover plays an essential role in cellular homeostasis by removing damaged organelles and unwanted cytoplasmic constituents, and is critical for plant defense and robust nutrient recycling, especially during nitrogen and fixed-carbon starvation and senescence. This ‘self eating’ is mediated by a conjugation system that modifies a pair of ubiquitin-fold proteins ATG12 and ATG8 to eventually form an autophagic vesicle coated with the ATG8-phosphatidylethanolamine (PE) adduct. ATG8-PE serves two purposes, one is to help shape the encapsulating vesicles and their subsequent fusion with the vacuole, and the other is to provide a docking platform for a suite of ATG8-interacting proteins that selectively tether appropriate cargo to the membrane surface before enclosure. In addition to bulk degradation, the ATG8 system is responsible for clearing organelles like mitochondria (mitophagy), chloroplasts (chlorophagy) and peroxisomes (pexophagy), and large cytoplasmic complexes such as 26S proteasomes (proteaphagy) or ribosomes (ribophagy) when dysfunctional or no longer needed. Using a multi-omics approach with maize, we are attempting to understand how autophagy regulates the metabolome and sculpts the proteome during normal growth and during nutrient starvation. Surprisingly, broad alterations in the leaf metabolome were evident in plants missing the core autophagy component ATG12 even without stress, particularly affecting products of lipid turnover and secondary metabolites, which were underpinned by substantial changes in the transcriptome and/or proteome. Cross-comparison of mRNA and protein abundances allowed for the identification of organelles, protein complexes, and individual proteins targeted for selective autophagic clearance, and revealed several processes controlled by this catabolism. During our work selective proteaphagy, we discovered that ubiquitylation of dysfunctional complexes followed by their recognition by the autophagy receptor RPN10 are key to this clearance. Surprisingly, further studies on RPN10 revealed that it represents the founding member of a new class of autophagy adaptors/receptors that uses a UIM instead of an AIM sequence for binding to ATG8. Assays with candidate UIM proteins and non-biased screens revealed that these adaptors/receptors are likely present in all eukaryotes. One family of UBX-UIM proteins are of particular interest as they help direct the degradation of the AAA-ATPase CDC48/p97 hexamer that couples ATP hydrolysis to the extraction and removal of damaged proteins associated with ER stress. With this new class of adaptors/receptors, we greatly extend the reach of selective autophagy and potentially identify new factors regulating autophagic vesicle dynamics.