Selective autophagy: ubiquitin-mediated recognition and beyond

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

Pankiv, S., Clausen, T. H., Lamark, T., Brech, A., Bruun, J.-A., Outzen, H., Øvervatn, A., Bjørkøy, G., & Johansen, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702824200 · Cited by 4,578 · see citing works

Parkin is recruited selectively to impaired mitochondria and promotes their autophagy

Narendra, D., Tanaka, A., Suen, D.-F., & Youle, R. J. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200809125 · Cited by 4,026 · see citing works

p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death

Bjørkøy, G., Lamark, T., Brech, A., Outzen, H., Perander, M., Øvervatn, A., Stenmark, H., & Johansen, T. (2005) · The Journal of Cell Biology · doi:10.1083/jcb.200507002 · Cited by 3,276 · see citing works

PINK1 Is Selectively Stabilized on Impaired Mitochondria to Activate Parkin

Narendra, D. P., Jin, S. M., Tanaka, A., Suen, D.-F., Gautier, C. A., Shen, J., Cookson, M. R., & Youle, R. J. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000298 · Cited by 2,944 · see citing works

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

Geisler, S., Holmström, K. M., Skujat, D., Fiesel, F. C., Rothfuss, O. C., Kahle, P. J., & Springer, W. (2010) · Nature Cell Biology · doi:10.1038/ncb2012 · Cited by 2,835 · see citing works

Impairment of the Ubiquitin-Proteasome System by Protein Aggregation

Bence, N., Sampat, R. M., & Kopito, R. R. (2001) · Science · doi:10.1126/science.292.5521.1552 · Cited by 2,192 · see citing works

Autophagosome formation: core machinery and adaptations

Xie, Z., & Klionsky, D. J. (2007) · Nature Cell Biology · doi:10.1038/ncb1007-1102 · Cited by 2,165 · see citing works

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

Komatsu, M., Waguri, S., Koike, M., Sou, Y.-S., Ueno, T., Hara, T., Mizushima, N., Iwata, J.-I., Ezaki, J., Murata, S., et al. (2007) · Cell · doi:10.1016/j.cell.2007.10.035 · Cited by 2,124 · see citing works

Impaired Degradation of Mutant α-Synuclein by Chaperone-Mediated Autophagy

Cuervo, A. M., Stefanis, L., Fredenburg, R., Lansbury, P. T., & Sulzer, D. (2004) · Science · doi:10.1126/science.1101738 · Cited by 2,024 · see citing works

Aggresomes, inclusion bodies and protein aggregation

Kopito, R. R. (2000) · Trends in Cell Biology · doi:10.1016/s0962-8924(00)01852-3 · Cited by 1,906 · see citing works

Drosophila pink1 is required for mitochondrial function and interacts genetically with parkin

Clark, I. E., Dodson, M. W., Jiang, C., Cao, J. H., Huh, J. R., Seol, J. H., Yoo, S. J., Hay, B. A., & Guo, M. (2006) · Nature · doi:10.1038/nature04779 · Cited by 1,788 · see citing works

FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells.

Zhao, J., Brault, J. J., Schild, A., Cao, P., Sandri, M., Schiaffino, S., Lecker, S. H., & Goldberg, A. L. (2007) · Cell Metabolism · doi:10.1016/j.cmet.2007.11.004 · Cited by 1,489 · see citing works

Nix is a selective autophagy receptor for mitochondrial clearance

Novak, I., Kirkin, V., McEwan, D. G., Zhang, J., Wild, P., Rozenknop, A., Rogov, V., Löhr, F., Popovic, D., Occhipinti, A., et al. (2010) · The EMBO Reports · doi:10.1038/embor.2009.256 · Cited by 1,309 · see citing works

HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS.

Pandey, U. B., Nie, Z., Batlevi, Y., McCray, B. A., Ritson, G. P., Nedelsky, N. B., Schwartz, S. L., DiProspero, N. A., Knight, M. A., Schuldiner, O., et al. (2007) · Nature · doi:10.1038/nature05853 · Cited by 1,234 · see citing works

A Role for NBR1 in Autophagosomal Degradation of Ubiquitinated Substrates

Kirkin, V., Lamark, T., Sou, Y., Bjørkøy, G., Nunn, J. A. L., Bruun, J., Shvets, E., McEwan, D. G., Clausen, T. H., Wild, P. S., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.020 · Cited by 1,158 · see citing works

The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria

Thurston, T. L. M., Ryzhakov, G., Bloor, S., von Muhlinen, N., & Randow, F. (2009) · Nature Immunology · doi:10.1038/ni.1800 · Cited by 872 · see citing works

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

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

HDAC6 and microtubules are required for autophagic degradation of aggregated huntingtin.

Iwata, A., Riley, B. E., Johnston, J. A., & Kopito, R. R. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508786200 · Cited by 719 · see citing works

Proteasome subunit Rpn13 is a novel ubiquitin receptor

Husnjak, K., Elsasser, S., Zhang, N., Chen, X., Randles, L., Shi, Y., Hofmann, K., Walters, K. J., Finley, D. J., & Đikić, I. (2008) · Nature · doi:10.1038/nature06926 · Cited by 662 · see citing works

Autophagy Inhibition Compromises Degradation of Ubiquitin-Proteasome Pathway Substrates

Korolchuk, V. I., Mansilla, A., Menzies, F. M., & Rubinsztein, D. C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.021 · Cited by 657 · see citing works

p62 Is a Common Component of Cytoplasmic Inclusions in Protein Aggregation Diseases

Zatloukal, K., Stumptner, C., Fuchsbichler, A., Heid, H., Schnoelzer, M., Kenner, L., Kleinert, R., Prinz, M., Aguzzi, A., & Denk, H. (2002) · The American Journal of Pathology · doi:10.1016/s0002-9440(10)64369-6 · Cited by 624 · see citing works

The Adaptor Protein p62/SQSTM1 Targets Invading Bacteria to the Autophagy Pathway

Zheng, Y. T., Shahnazari, S., Brech, A., Lamark, T., Johansen, T., & Brumell, J. H. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900441 · Cited by 581 · see citing works

Chaperone-Assisted Selective Autophagy Is Essential for Muscle Maintenance

Arndt, V., Dick, N., Tawo, R., Dreiseidler, M., Wenzel, D., Hesse, M., Fürst, D. O., Säftig, P., Saint, R. B., Fleischmann, B. K., et al. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.022 · Cited by 572 · see citing works

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

Protein quality control during aging involves recruitment of the macroautophagy pathway by BAG3

Gamerdinger, M., Hajieva, P., Kaya, A. M., Wolfrum, U., Hartl, F. U., & Behl, C. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.29 · Cited by 522 · cited 1× · see citing works

Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway.

Harding, T. M., Morano, K. A., Scott, S. V., & Klionsky, D. J. (1995) · The Journal of Cell Biology · doi:10.1083/jcb.131.3.591 · Cited by 503 · 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

Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae

Suzuki, K., & Ohsumi, Y. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.01.096 · Cited by 394 · see citing works

Delivery of ubiquitinated substrates to protein-unfolding machines

Elsasser, S., & Finley, D. J. (2005) · Nature Cell Biology · doi:10.1038/ncb0805-742 · Cited by 364 · see citing works

HspB8 Chaperone Activity toward Poly(Q)-containing Proteins Depends on Its Association with Bag3, a Stimulator of Macroautophagy

Carra, S., Seguin, S. J., Lambert, H., & Landry, J. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m706304200 · Cited by 347 · see citing works

Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6

Olzmann, J. A., Li, L., Chudaev, M. V., Chen, J., Perez, F. A., Palmiter, R. D., & Chin, L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200611128 · Cited by 335 · see citing works

p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy

Clausen, T. H., Lamark, T., Isakson, P., Finley, K. D., Larsen, K. B., Brech, A., Øvervatn, A., Stenmark, H., Bjørkøy, G., Simonsen, A., et al. (2010) · Autophagy · doi:10.4161/auto.6.3.11226 · Cited by 321 · see citing works

Microtubules Support Production of Starvation-induced Autophagosomes but Not Their Targeting and Fusion with Lysosomes

Fass, E., Shvets, E., Degani, I., Hirschberg, K., & Elazar, Z. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m607031200 · Cited by 286 · see citing works

Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes

Simonsen, A., Birkeland, H. C. G., Gillooly, D. J., Mizushima, N., Kuma, A., Yoshimori, T., Slagsvold, T., Brech, A., & Stenmark, H. (2004) · Journal of Cell Science · doi:10.1242/jcs.01287 · Cited by 282 · see citing works

HDAC6–p97/VCP controlled polyubiquitin chain turnover

Boyault, C., Gilquin, B., Zhang, Y., Rybin, V., Garman, E. F., Meyer‐Klaucke, W., Matthias, P., Müller, C. W., & Khochbin, S. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601210 · Cited by 270 · see citing works

Cvt19 Is a Receptor for the Cytoplasm-to-Vacuole Targeting Pathway

Scott, S. V., Guan, J., Hutchins, M. U., Kim, J., & Klionsky, D. J. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00263-5 · Cited by 269 · see citing works

Midbody ring disposal by autophagy is a post-abscission event of cytokinesis

Pohl, C., & Jentsch, S. (2008) · Nature Cell Biology · doi:10.1038/ncb1813 · Cited by 197 · see citing works

Increased expression of p62 in expanded polyglutamine‐expressing cells and its association with polyglutamine inclusions

Nagaoka, U., Kim, K., Jana, N. R., Doi, H., Maruyama, M., Mitsui, K., Oyama, F., & Nukina, N. (2004) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2004.02692.x · Cited by 183 · see citing works

Pathogenetic mechanisms of parkin in Parkinson's disease

Hattori, N., & Mizuno, Y. (2004) · The Lancet · doi:10.1016/s0140-6736(04)16901-8 · Cited by 162 · see citing works

Selective types of autophagy in yeast.

Kraft, C., Reggiori, F., & Peter, M. (2009) · Biochimica et Biophysica Acta · doi:10.1016/j.bbamcr.2009.02.006 · Cited by 158 · see citing works

Vacuolar Localization of Oligomeric α-Mannosidase Requires the Cytoplasm to Vacuole Targeting and Autophagy Pathway Components in Saccharomyces cerevisiae

Hutchins, M. U., & Klionsky, D. J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101150200 · Cited by 157 · see citing works

Ubiquitin-binding domains and their role in the DNA damage response

Hofmann, K. (2009) · DNA repair · doi:10.1016/j.dnarep.2009.01.003 · Cited by 142 · see citing works

Parkin: a multifaceted ubiquitin ligase

Moore, D. J. (2006) · Biochemical Society Transactions · doi:10.1042/bst0340749 · Cited by 119 · see citing works

Peroxisome Size Provides Insights into the Function of Autophagy-related Proteins

Nazarko, T. Y., Farré, J., & Subramani, S. E. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e09-03-0221 · Cited by 75 · see citing works

Autophagy in immunity and inflammation

Levine, B., Mizushima, N., & Virgin, H. W. (2011) · Nature · doi:10.1038/nature09782 · Cited by 3,289 · see citing works

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

Wild, P., Farhan, H., McEwan, D. G., Wagner, S., Rogov, V. V., Brady, N. R., Richter, B., Korac, J., Waidmann, O., Choudhary, C., et al. (2011) · Science · doi:10.1126/science.1205405 · Cited by 1,298 · see citing works

Cargo recognition and trafficking in selective autophagy

Stolz, A., Ernst, A., & Dikic, I. (2014) · Nature Cell Biology · doi:10.1038/ncb2979 · Cited by 1,207 · see citing works

Atg8: an autophagy-related ubiquitin-like protein family.

Shpilka, T., Weidberg, H., Pietrokovski, S., & Elazar, Z. (2011) · Genome biology · doi:10.1186/gb-2011-12-7-226 · Cited by 543 · see citing works

Autophagy Protects the Proximal Tubule from Degeneration and Acute Ischemic Injury

Kimura, T., Takabatake, Y., Takahashi, A., Kaimori, J.-Y., Matsui, I., Namba, T., Kitamura, H., Niimura, F., Matsusaka, T., Soga, T., et al. (2011) · Journal of the American Society of Nephrology · doi:10.1681/asn.2010070705 · Cited by 461 · see citing works

Biogenesis and Cargo Selectivity of Autophagosomes

Weidberg, H., Shvets, E., & Elazar, Z. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052709-094552 · Cited by 466 · see citing works

Autophagy in the renewal, differentiation and homeostasis of immune cells

Clarke, A. J., & Simon, A. K. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-018-0095-2 · Cited by 361 · see citing works

Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome

Bourdenx, M., Martín-Segura, A., Scrivo, A., Rodriguez-Navarro, J. A., Kaushik, S., Tasset, I., Diaz, A., Storm, N. J., Xin, Q., Juste, Y. R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.048 · Cited by 337 · see citing works

Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates

Korac, J., Schaeffer, V., Kovacevic, I., Clement, A. M., Jungblut, B., Behl, C., Terzic, J., & Dikic, I. (2013) · Journal of Cell Science · doi:10.1242/jcs.114926 · Cited by 336 · see citing works

Potential function for the Huntingtin protein as a scaffold for selective autophagy

Ochaba, J., Lukacsovich, T., Csikos, G., Zheng, S., Margulis, J., Salazar, L., Mao, K., Lau, A. L., Yeung, S. Y., Humbert, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420103111 · Cited by 308 · see citing works

How mitochondrial dynamism orchestrates mitophagy

Shirihai, O. S., Song, M., & Dorn, G. W. (2015) · Circulation Research · doi:10.1161/circresaha.116.306374 · Cited by 311 · see citing works

Histone deacetylase 6–mediated selective autophagy regulates COPD-associated cilia dysfunction

Lam, H. C., Cloonan, S. M., Bhashyam, A. R., Haspel, J. A., Singh, A., Sathirapongsasuti, J. F., Cervo, M., Yao, H., Chung, A. L., Mizumura, K., et al. (2013) · Journal of Clinical Investigation · doi:10.1172/jci69636 · Cited by 307 · see citing works

Autophagy Guards Against Cisplatin-Induced Acute Kidney Injury

Takahashi, A., Kimura, T., Takabatake, Y., Namba, T., Kaimori, J., Kitamura, H., Matsui, I., Niimura, F., Matsusaka, T., Fujita, N., et al. (2012) · The American Journal of Pathology · doi:10.1016/j.ajpath.2011.11.001 · Cited by 253 · see citing works

Autophagy variation within a cell population determines cell fate through selective degradation of Fap-1

Gump, J. M., Staskiewicz, L., Morgan, M. J., Bamberg, A., Riches, D. W. H., & Thorburn, A. (2014) · Nature Cell Biology · doi:10.1038/ncb2886 · Cited by 230 · see citing works

Mitochondrial abnormalities in temporal lobe of autistic brain

Tang, G., Gutierrez Rios, P., Kuo, S.-H., Akman, H. O., Rosoklija, G., Tanji, K., Dwork, A., Schon, E. A., DiMauro, S., Goldman, J., et al. (2013) · Neurobiology of Disease · doi:10.1016/j.nbd.2013.01.006 · Cited by 194 · see citing works

Role of p62/SQSTM1 in liver physiology and pathogenesis

Manley, S., Williams, J. A., & Ding, W.-X. (2013) · Experimental Biology and Medicine · doi:10.1177/1535370213489446 · Cited by 135 · see citing works

Targeting Lysosomal Degradation Pathways: New Strategies and Techniques for Drug Discovery

Pei, J., Wang, G., Feng, L., Zhang, J., Jiang, T., Sun, Q., & Ouyang, L. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01689 · Cited by 124 · see citing works

Protein arginine methyltransferase 5 has prognostic relevance and is a druggable target in multiple myeloma

Gullà, A., Hideshima, T., Bianchi, G., Fulciniti, M., Kemal Samur, M., Qi, J., Tai, Y.-T., Harada, T., Morelli, E., Amodio, N., et al. (2018) · Leukemia · doi:10.1038/leu.2017.334 · Cited by 102 · see citing works

Toward an integrative view of Optineurin functions

Kachaner, D., Génin, P., Laplantine, E., & Weil, R. (2012) · Cell Cycle · doi:10.4161/cc.20946 · Cited by 99 · see citing works

Spaceflight Activates Autophagy Programs and the Proteasome in Mouse Liver

Blaber, E., Pecaut, M., & Jonscher, K. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18102062 · Cited by 70 · see citing works

Depletion of p62 reduces nuclear inclusions and paradoxically ameliorates disease phenotypes in Huntington's model mice

Kurosawa, M., Matsumoto, G., Kino, Y., Okuno, M., Kurosawa-Yamada, M., Washizu, C., Taniguchi, H., Nakaso, K., Yanagawa, T., Warabi, E., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddu522 · Cited by 63 · see citing works

Cell senescence as both a dynamic and a static phenotype

Young, A. R. J., Narita, M., & Narita, M. (2013) · Methods in Molecular Biology · doi:10.1007/978-1-62703-239-1_1 · Cited by 50 · see citing works

Neuronal nucleus and cytoplasm volume deficit in children with autism and volume increase in adolescents and adults

Wegiel, J., Flory, M., Kuchna, I., Nowicki, K., Ma, S. Y., Imaki, H., Wegiel, J., Frackowiak, J., Kolecka, B. M., Wierzba-Bobrowicz, T., et al. (2015) · Acta Neuropathologica Communications · doi:10.1186/s40478-015-0183-5 · Cited by 47 · see citing works

Overexpression of pink1 or parkin in indirect flight muscles promotes mitochondrial proteostasis and extends lifespan in Drosophila melanogaster

Si, H., Ma, P., Liang, Q., Yin, Y., Wang, P., Zhang, Q., Wang, S., & Deng, H. (2019) · PLOS ONE · doi:10.1371/journal.pone.0225214 · Cited by 37 · see citing works

E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer

Eletr, Z. M., Huang, D. T. C., Duda, D. M., Schulman, B. A., & Kuhlman, B. A. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb984 · Cited by 167 · see citing works

Alternative Ubiquitin Activation/Conjugation Cascades Interact with N-End Rule Ubiquitin Ligases to Control Degradation of RGS Proteins

Lee, P. C.-W., Sowa, M. E., Gygi, S. P., & Harper, J. W. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.05.034 · Cited by 75 · see citing works

U-box proteins as a new family of ubiquitin ligases

Hatakeyama, S., & Nakayama, K. I. (2003) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(03)00245-6 · Cited by 264 · see citing works

Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes

Liu, X., Zhao, B., Sun, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14286 · Cited by 48 · see citing works

Human ubiquitin-protein ligase Nedd4 : expression, subcellular localization, and selective interaction with ubiquitin-conjugating enzymes

阿南, 正. (1999) · Medical Entomology and Zoology · doi:10.11501/3166058