Highlights d Quantitative global proteomics of cells during nutrient stress d TEX264 identified as ER-associated selective autophagy receptor during starvation d TEX264 traffics into autophagosomes at ER tubule junctions d TEX264-deficient cells defective in ER-phagy during nutrient stress

Highlights d Global phospho and ubiquitylome analysis of PINK1-Parkin pathway in iNeurons d Dynamics and specificity of Parkin-mediated ubiquitylation revealed in iNeurons d p97-mediated MFN turnover not required for Parkin substrate ''gating'' in iNeurons d USP30 acts primarily on translocon and supports import quality control in iNeurons

Ribosomes are abundant cellular machines1,2 regulated by assembly, supernumerary subunit turnover, and nascent chain quality control mechanisms1–5. Moreover, nitrogen starvation in yeast has been reported to promote selective ribosome delivery to the vacuole in an autophagy conjugation system-dependent manner, a process called “ribophagy”6,7. However, whether ribophagy in mammals is selective or regulated is unclear. Using Ribo-Keima flux reporters, we find that starvation or mTOR inhibition promotes VPS34-dependent ribophagic flux, which unlike yeast, is largely ATG8 conjugation independent and occurs concomitantly with other cytosolic protein autophagic flux reporters8,9. Ribophagic flux was not induced upon inhibition of translational elongation or nascent chain uncoupling, but was induced in a comparatively selective manner upon proteotoxic stress via arsenite10 or chromosome mis-segregation11 dependent upon VPS34 and ATG8 conjugation. Unexpectedly, agents typically used to induce selective autophagy also promoted increased ribosome and cytosolic protein reporter flux, suggesting significant bulk or “by-stander” autophagy during what is often considered selective autophagy12,13. These results emphasize the importance of monitoring non-specific cargo flux when assessing selective autophagy pathways.