Panse, V. G. & Johnson, A. W. Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem. Sci. 35, 260–266 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

López, A. R. et al. Autophagy-mediated control of ribosome homeostasis in oncogene-induced senescence. Cell Rep. 42, 113381 (2023).

Article  PubMed  Google Scholar 

Kazibwe, Z., Liu, A. Y., MacIntosh, G. C. & Bassham, D. C. The ins and outs of autophagic ribosome turnover. Cells 8, 1603 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kraft, C., Deplazes, A., Sohrmann, M. & Peter, M. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat. Cell Biol. 10, 602–610 (2008).

Article  CAS  PubMed  Google Scholar 

Wyant, G. A. et al. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science 360, 751–758 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yuan, M. et al. Cancer-associated fibroblasts employ NUFIP1-dependent autophagy to secrete nucleosides and support pancreatic tumor growth. Nat. Cancer 3, 945–960 (2022).

Article  CAS  PubMed  Google Scholar 

Mi, H. Y. et al. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 49, D394–D403 (2021).

Article  CAS  PubMed  Google Scholar 

Wilfling, F. et al. A selective autophagy pathway for phase-separated endocytic protein deposits. Mol. Cell 80, 764–778 e767 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tu, W. Y., Huang, Y. C., Liu, L. F., Chang, L. H. & Tam, M. F. Rpl12p affects the transcription of the PHO pathway high-affinity inorganic phosphate transporters and repressible phosphatases. Yeast 28, 481–493 (2011).

Article  CAS  PubMed  Google Scholar 

Yorimitsu, T. & Klionsky, D. J. Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol. Biol. Cell 16, 1593–1605 (2005).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Johansen, T. & Lamark, T. Selective autophagy: ATG8 family proteins, LIR motifs and cargo receptors. J. Mol. Biol. 432, 80–103 (2020).

Article  CAS  PubMed  Google Scholar 

Jacomin, A. C., Samavedam, S., Promponas, V. & Nezis, I. P. iLIR database: a web resource for LIR motif-containing proteins in eukaryotes. Autophagy 12, 1945–1953 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6, 917–922 (2009).

Article  CAS  PubMed  Google Scholar 

Mochida, K. et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 522, 359–362 (2015).

Article  CAS  PubMed  Google Scholar 

Huang, H. et al. Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast. EMBO J. 34, 154–168 (2015).

Article  CAS  PubMed  Google Scholar 

Noda, T. & Ohsumi, Y. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J. Biol. Chem. 273, 3963–3966 (1998).

Article  CAS  PubMed  Google Scholar 

Yi, C. et al. Formation of a Snf1–Mec1–Atg1 Module on Mitochondria Governs Energy Deprivation-Induced Autophagy by Regulating Mitochondrial Respiration. Dev. Cell 41, 59–71.e54 (2017).

Article  CAS  PubMed  Google Scholar 

Matsuura, A., Tsukada, M., Wada, Y. & Ohsumi, Y. Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192, 245–250 (1997).

Article  CAS  PubMed  Google Scholar 

Allen, J. J. et al. A semisynthetic epitope for kinase substrates. Nat. Methods 4, 511–516 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chasse, H., Boulben, S., Costache, V., Cormier, P. & Morales, J. Analysis of translation using polysome profiling. Nucleic Acids Res. 45, e15 (2017).

PubMed  Google Scholar 

Li, H., He, C. W., Zhu, J. & Xie, Z. A validated set of ascorbate peroxidase-based organelle markers for electron microscopy of Saccharomyces cerevisiae. mSphere 7, e0010722 (2022).

Article  PubMed  Google Scholar 

Tsukada, M. & Ohsumi, Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 333, 169–174 (1993).

Article  CAS  PubMed  Google Scholar 

Palmisano, N. J. & Melendez, A. Autophagy in C. elegans development. Dev. Biol. 447, 103–125 (2019).

Article  CAS  PubMed  Google Scholar 

Lin, L. et al. The scaffold protein EPG-7 links cargo receptor complexes with the autophagic assembly machinery. J. Cell Biol. 201, 113–129 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun, T., Wang, X., Lu, Q., Ren, H. & Zhang, H. CUP-5, the C. elegans ortholog of the mammalian lysosomal channel protein MLN1/TRPML1, is required for proteolytic degradation in autolysosomes. Autophagy 7, 1308–1315 (2011).

Article  CAS  PubMed  Google Scholar 

Zheng, Z. et al. GABAergic synapses suppress intestinal innate immunity via insulin signaling in Caenorhabditis elegans. PNAS 118, e2021063118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kenyon, C., Chang, J., Gensch, E., Rudner, A. & Tabtiang, R. A C. elegans mutant that lives twice as long as wild-type. Nature 366, 461–464 (1993).

Article  CAS  PubMed  Google Scholar 

Jipa, A. et al. Analysis of Drosophila Atg8 proteins reveals multiple lipidation-independent roles. Autophagy 17, 2565–2575 (2021).

Article  CAS  PubMed  Google Scholar 

Bar, S., Prasad, M. & Datta, R. Neuromuscular degeneration and locomotor deficit in a Drosophila model of mucopolysaccharidosis VII is attenuated by treatment with resveratrol. Dis. Model Mech. 11, dmm036954 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tan, W., Schauder, C., Naryshkina, T., Minakhina, S. & Steward, R. Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function. Dev. Biol. 410, 202–212 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Martens, S. & Fracchiolla, D. Activation and targeting of ATG8 protein lipidation. Cell Discov. 6, 23 (2020).

Article  CAS