Cargo recognition and trafficking in selective autophagy

A role for mitochondria in nlrp3 inflammasome activation

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p62/SQSTM1 Binds Directly to Atg8/LC3 to Facilitate Degradation of Ubiquitinated Protein Aggregates by Autophagy

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Parkin is recruited selectively to impaired mitochondria and promotes their autophagy

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Autophagy in immunity and inflammation

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Autophagy proteins regulate innate immune responses by inhibiting the release of mitochondrial DNA mediated by the NALP3 inflammasome

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The Role of Atg Proteins in Autophagosome Formation

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PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1

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Mitofusin 2 tethers endoplasmic reticulum to mitochondria

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Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice.

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Eaten alive: a history of macroautophagy

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Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum

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Isolation and characterization of autophagy‐defective mutants of Saccharomyces cerevisiae

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Autophagosomes form at ER–mitochondria contact sites

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Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells

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ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase

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ULK1·ATG13·FIP200 Complex Mediates mTOR Signaling and Is Essential for Autophagy

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Network organization of the human autophagy system

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A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

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Mitochondria Supply Membranes for Autophagosome Biogenesis during Starvation

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PINK1-Phosphorylated Mitofusin 2 Is a Parkin Receptor for Culling Damaged Mitochondria

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Nix is a selective autophagy receptor for mitochondrial clearance

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The autophagosome: origins unknown, biogenesis complex

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Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry

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Phosphorylation of the Autophagy Receptor Optineurin Restricts <i>Salmonella</i> Growth

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A Role for Ubiquitin in Selective Autophagy

Kirkin, V., McEwan, D. G., Novak, I., & Đikić, I. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.04.026 · Cited by 1,227 · see citing works

Atg8, a Ubiquitin-like Protein Required for Autophagosome Formation, Mediates Membrane Tethering and Hemifusion

Nakatogawa, H., Ichimura, Y., & Ohsumi, Y. (2007) · Cell · doi:10.1016/j.cell.2007.05.021 · Cited by 1,215 · see citing works

Essential role for Nix in autophagic maturation of erythroid cells

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A Role for NBR1 in Autophagosomal Degradation of Ubiquitinated Substrates

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A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation

Hayashi, M., Fujita, N., Noda, T., Yamaguchi, A., Yoshimori, T., & Yamamoto, A. (2009) · Nature Cell Biology · doi:10.1038/ncb1991 · Cited by 1,050 · see citing works

The pre‐autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation

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Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion

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Role of BNIP3 and NIX in cell death, autophagy, and mitophagy

Zhang, J., & Ney, P. A. (2009) · Cell Death &amp; Differentiation · doi:10.1038/cdd.2009.16 · Cited by 1,021 · see citing works

Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization

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Autophagy‐based unconventional secretory pathway for extracellular delivery of IL‐1β

Dupont, N., Jiang, S., Pilli, M., Ornatowski, W., Bhattacharya, D., & Deretic, V. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.398 · Cited by 967 · see citing works

Mitofusin 1 and mitofusin 2 are ubiquitinated in a PINK1/parkin-dependent manner upon induction of mitophagy

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Mitochondria-Anchored Receptor Atg32 Mediates Degradation of Mitochondria via Selective Autophagy

Okamoto, K., Kondo‐Okamoto, N., & Ohsumi, Y. (2009) · Developmental Cell · doi:10.1016/j.devcel.2009.06.013 · Cited by 867 · see citing works

Atg32 Is a Mitochondrial Protein that Confers Selectivity during Mitophagy

Kanki, T., Wang, K., Cao, Y., Baba, M., & Klionsky, D. J. (2009) · Developmental Cell · doi:10.1016/j.devcel.2009.06.014 · Cited by 798 · see citing works

p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both

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LC3 and GATE‐16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis

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GABAA-receptor-associated protein links GABAA receptors and the cytoskeleton

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Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease

Kraft, C., Deplazes, A., Sohrmann, M., & Peter, M. (2008) · Nature Cell Biology · doi:10.1038/ncb1723 · Cited by 733 · see citing works

Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation

Polson, H. E. J., de Lartigue, J., Rigden, D. J., Reedijk, M., Urbé, S., Clague, M. J., & Tooze, S. A. (2010) · Autophagy · doi:10.4161/auto.6.4.11863 · Cited by 712 · see citing works

Serine 403 Phosphorylation of p62/SQSTM1 Regulates Selective Autophagic Clearance of Ubiquitinated Proteins

Matsumoto, G., Wada, K., Okuno, M., Kurosawa, M., & Nukina, N. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.07.039 · Cited by 692 · see citing works

3D tomography reveals connections between the phagophore and endoplasmic reticulum

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Atg9 vesicles are an important membrane source during early steps of autophagosome formation

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TBK-1 Promotes Autophagy-Mediated Antimicrobial Defense by Controlling Autophagosome Maturation

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Selective autophagy: ubiquitin-mediated recognition and beyond

Kraft, C., Peter, M., & Hofmann, K. (2010) · Nature Cell Biology · doi:10.1038/ncb0910-836 · Cited by 639 · see citing works

Hypoxia-induced autophagy: cell death or cell survival?

Mazure, N. M., & Pouysségur, J. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.11.015 · Cited by 620 · see citing works

Formation and function of phosphatidylserine and phosphatidylethanolamine in mammalian cells

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Nix Is Critical to Two Distinct Phases of Mitophagy, Reactive Oxygen Species-mediated Autophagy Induction and Parkin-Ubiquitin-p62-mediated Mitochondrial Priming

Ding, W.-X., Ni, H., Li, M., Liao, Y., Chen, X., Stolz, D. B., Dorn, G. W., & Yin, X. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.119537 · Cited by 586 · see citing works

PI(4,5)P2-Dependent and Ca2+-Regulated ER-PM Interactions Mediated by the Extended Synaptotagmins

Giordano, F., Saheki, Y., Idevall‐Hagren, O., Colombo, S. F., Pirruccello, M., Milošević, I., Gracheva, E. O., Bagriantsev, S. N., Borgese, N., & Camilli, P. V. D. (2013) · Cell · doi:10.1016/j.cell.2013.05.026 · Cited by 580 · see citing works

Ulk1 plays a critical role in the autophagic clearance of mitochondria and ribosomes during reticulocyte maturation

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Isolation of autophagocytosis mutants of Saccharomyces cerevisiae

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Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes

Kim, P. K., Hailey, D. W., Mullen, R. T., & Lippincott‐Schwartz, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810611105 · Cited by 533 · see citing works

Modulation of Serines 17 and 24 in the LC3-interacting Region of Bnip3 Determines Pro-survival Mitophagy versus Apoptosis

Zhu, Y., Maßen, S., Terenzio, M., Lang, V., Chen-Lindner, S., Eils, R., Novak, I., Đikić, I., Hamacher‐Brady, A., & Brady, N. R. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.399345 · Cited by 491 · see citing works

Autophagy Proteins Regulate the Secretory Component of Osteoclastic Bone Resorption

DeSelm, C. J., Miller, B. C., Zou, W., Beatty, W. L., van Meel, E., Takahata, Y., Klumperman, J., Tooze, S. A., Teitelbaum, S. L., & Virgin, H. W. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.08.016 · Cited by 487 · see citing works

Autophagy machinery mediates macroendocytic processing and entotic cell death by targeting single membranes

Florey, O., Kim, S. E., Sandoval, C. P., Haynes, C. M., & Overholtzer, M. (2011) · Nature Cell Biology · doi:10.1038/ncb2363 · Cited by 459 · see citing works

The Selective Macroautophagic Degradation of Aggregated Proteins Requires the PI3P-Binding Protein Alfy

Filimonenko, M., Isakson, P., Finley, K. D., Anderson, M. R., Jeong, H., Melia, T. J., Bartlett, B. J., Myers, K. M., Birkeland, H. C. G., Lamark, T., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.04.007 · Cited by 432 · see citing works

Diverse Autophagosome Membrane Sources Coalesce in Recycling Endosomes

Puri, C., Renna, M., Bento, C. F., Moreau, K., & Rubinsztein, D. C. (2013) · Cell · doi:10.1016/j.cell.2013.08.044 · Cited by 423 · see citing works

p62 targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding

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An Atg1/Atg13 Complex with Multiple Roles in TOR-mediated Autophagy Regulation

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TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes

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Ref(2)P, the <i>Drosophila melanogaster</i> homologue of mammalian p62, is required for the formation of protein aggregates in adult brain

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NBR1 acts as an autophagy receptor for peroxisomes

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PpAtg30 Tags Peroxisomes for Turnover by Selective Autophagy

Farré, J.-C., Manjithaya, R., Mathewson, R. D., & Subramani, S. (2008) · Developmental Cell · doi:10.1016/j.devcel.2007.12.011 · Cited by 331 · see citing works

Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy

Yamano, K., Fogel, A. I., Wang, C., van der Bliek, A. M., & Youle, R. J. (2014) · eLife · doi:10.7554/elife.01612 · Cited by 307 · see citing works

Impaired mitochondrial transport and Parkin-independent degeneration of respiratory chain-deficient dopamine neurons in vivo

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p62 and NDP52 Proteins Target Intracytosolic Shigella and Listeria to Different Autophagy Pathways

Mostowy, S., Sancho-Shimizu, V., Hamon, M. A., Simeone, R., Brosch, R., Johansen, T., & Cossart, P. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.223610 · Cited by 294 · see citing works

Early endosomes and endosomal coatomer are required for autophagy

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Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy

Lynch-Day, M. A., Bhandari, D., Menon, S., Huang, J., Cai, H., Bartholomew, C. R., Brumell, J. H., Ferro‐Novick, S., & Klionsky, D. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000063107 · Cited by 278 · see citing works

Convergence of Multiple Autophagy and Cytoplasm to Vacuole Targeting Components to a Perivacuolar Membrane Compartment Prior tode Novo Vesicle Formation

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ATGGenes Involved in Non-Selective Autophagy are Conserved from Yeast to Man, but the Selective Cvt and Pexophagy Pathways also Require Organism-Specific Genes

Meijer, W. H., van der Klei, I. J., Marten Veenhuis, A., & Kiel, J. A. K. W. (2007) · Autophagy · doi:10.4161/auto.3595 · Cited by 261 · see citing works

Rheb Regulates Mitophagy Induced by Mitochondrial Energetic Status

Melser, S., Chatelain, É. H., Lavie, J., Mahfouf, W., José, C., Obre, É., Goorden, S. M. I., Priault, M., Elgersma, Y., Rezvani, H. R., et al. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.03.014 · Cited by 259 · see citing works

The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy

Rawet-Slobodkin, M., & Elazar, Z. (2013) · Essays in Biochemistry · doi:10.1042/bse0550051 · Cited by 259 · see citing works

Neutral Lipid Stores and Lipase PNPLA5 Contribute to Autophagosome Biogenesis

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The LC3 interactome at a glance

Wild, P. S., McEwan, D. G., & Đikić, I. (2013) · Journal of Cell Science · doi:10.1242/jcs.140426 · Cited by 250 · see citing works

GATE‐16, a membrane transport modulator, interacts with NSF and the Golgi v‐SNARE GOS‐28

Sagiv, Y., Legesse‐Miller, A., Porat, A., & Elazar, Z. (2000) · The EMBO Journal · doi:10.1093/emboj/19.7.1494 · Cited by 240 · see citing works

An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase

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Adaptor complex AP2/PICALM, through interaction with LC3, targets Alzheimer's APP-CTF for terminal degradation via autophagy

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AMP-Activated Protein Kinase: A Universal Regulator of Autophagy?

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The Subcellular Distribution of GABARAP and Its Ability to Interact with NSF Suggest a Role for This Protein in the Intracellular Transport of GABAA Receptors

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Biogenesis of a novel compartment for autophagosome-mediated unconventional protein secretion

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The ubiquitin-binding adaptor proteins p62/SQSTM1 and NDP52 are recruited independently to bacteria-associated microdomains to target Salmonella to the autophagy pathway

Cemma, M., Kim, P. K., & Brumell, J. H. (2011) · Autophagy · doi:10.4161/auto.7.3.14046 · Cited by 203 · see citing works

ER–PM connections: sites of information transfer and inter-organelle communication

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Modulation of Local PtdIns3P Levels by the PI Phosphatase MTMR3 Regulates Constitutive Autophagy

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Rab GTPase-Activating Proteins in Autophagy: Regulation of Endocytic and Autophagy Pathways by Direct Binding to Human ATG8 Modifiers

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