[1] N. Mizushima and M. Komatsu, “Autophagy : renovation of cells and tissues,” Cell, vol. 147, no. 4, p. 728–741, 2011.
[2] C. A. Lamb, T. Yoshimori, and S. A. Tooze, “The autophagosome: origins unknown, biogenesis complex,” Nat. Rev. Mol. Cell Biol., vol. 14, no. 12, p. 759–774, 2013.
[3] A. Abada and Z. Elazar, “Getting ready for building: signaling and autophagosome biogenesis,” EMBO Rep., vol. 15, no. 8, p. 839–852, 2014.
[4] T. N. Nguyen, B. S. Padman, J. Usher, V. Oorschot, G. Ramm, and M. Lazarou, “Atg8 family LC3/GABARAP proteins are crucial for autophagosome–lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation,” J. Cell Biol., vol. 215, no. 6, p. 857–874, 2016.
[5] A. Stolz, A. Ernst, and I. Dikic, “Cargo recognition and trafficking in selective autophagy,” Nat. Cell Biol., vol. 16, no. 6, p. 495–501, 2014.
[6] J. Sawa-Makarska, C. Abert, J. Romanov, B. Zens, I. Ibiricu, and S. Martens, “Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy,” Nat. Cell Biol., vol. 16, no. 5, p. 425–433, 2014.
[7] M. Manil-Ségalen, C. Lefebvre, C. Jenzer, M. Trichet, C. Boulogne, B. Satiat-Jeunemaitre, and R. Legouis, “The C.elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39,” Dev. Cell, vol. 28, no. 1, p. 43–55, 2014.
[8] E. Itakura, C. Kishi-Itakura, I. Koyama-Honda, and N. Mizushima, “Structures containing Atg9A and the ULK1 complex independently target depolarized mitochondria at initial stages of Parkin-mediated mitophagy,” J. Cell Sci., vol. 125, no. 6, p. 1488–1499, 2012.
[9] H. Weidberg, T. Shpilka, E. Shvets, A. Abada, F. Shimron, and Z. Elazar, “LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis,” Dev. Cell, vol. 20, no. 4, p. 444–454, 2011.
[10] H. Weidberg, E. Shvets, T. Shpilka, F. Shimron, V. Shinder, and Z. Elazar, “LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis,” EMBO J., vol. 29, no. 11, p. 1792–1802, 2010.
[11] N. Fujita, M. Hayashi-Nishino, H. Fukumoto, H. Omori, A. Yamamoto, and T. Yoshimori, “An Atg4B mutant hampers the lipidation of LC3paralogues and causes defects in autophagosome closure,” Mol Biol Cell, vol. 19, no. 11, p. 4651–4659, 2008.
[12] H. Nakatogawa, Y. Ichimura, and Y. Ohsumi, “Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion,” Cell, vol. 130, no. 1, p. 165–178, 2007.
[13] K. Tsuboyama, I. Koyama-Honda, Y. Sakamaki, M. Koike, H. Morishita, and N. Mizushima, “The ATG conjugation systems are important for degradation of the inner autophagosomal membrane,” Science, vol. 354, no. 6315, p. 1036–1041, 2016.
[14] Y. Takahashi, H. He, Z. Tang, T. Hattori, Y. Liu, M. M. Young, J. M. Serfass, L. Chen, M. Gebru, C. Chen, C. A. Wills, J. M. Atkinson, H. Chen, T. Abraham, and H. G. Wang, “An autophagy assay reveals the ESCRT-III component CHMP2A as a regulator of phagophore closure,” Nat. Commun., vol. 9, no. 1, 2018.
[15] E. Itakura, C. Kishi-Itakura, and N. Mizushima, “The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes,” Cell, vol. 151, no. 6, p. 1256–1269, 2012.
[16] T. Matsui, P. Jiang, S. Nakano, Y. Sakamaki, H. Yamamoto, and N. Mizushima, “Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17,” J. Cell Biol., vol. 217, no. 8, pp. 2633-2645, 2018.
[17] L. Bas, D. Papinski, M. Licheva, R. Torggler, S. Rohringer, M. Schuschnig, and C. Kraft, “Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome–vacuole fusion,” J. Cell Biol., vol. 217, no. 10, p. 3656-3669, 2018.
[18] J. Gao, F. Reggiori, and C. Ungermann, “A novel in vitro assay reveals SNARE topology and the role of Ykt6 in autophagosome fusion with vacuoles,” J. Cell Biol., vol. 217, no. 10, p. 3670-3682, 2018.
[19] N. Mizushima, “A brief history of autophagy from cell biology to physiology and disease,” Nat. Cell Biol., vol. 20, no. 5, p. 521-527, 2018
[20] M. Tsukada and Y. Ohsumi, “Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae,” FEBS Lett., vol. 333, no. 1–2, p. 169–174, 1993.
[21] M. Thumma, R. Egner, B. Koch, M. Schlumpberger, M. Straub, M. Veenhuisb, and D. H. Wolf, “Isolation of autophagocytosis mutants of Saccharomyces cerevisiae,” FEBS Lett., vol. 349, no. 2, p. 275–280, 1994.
[22] T. M. Harding, K. A. Morano, S. V Scott, and D. J. Klionsky, “Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway,” J. Cell Biol., vol. 13, no. 3, p. 591–602, 1995.
[23] P. E. Strømhaug, A. Bevan, and W. A. Dunn, “GSA11 encodes a unique 208-kDa protein required for pexophagy and autophagy in Pichia pastoris,” J. Biol. Chem., vol. 276, no. 45, p. 42422–42435, 2001.
[24] R. van Dijk, K. N. Faber, A. T. Hammond, B. S. Glick, M. Veenhuis, and J. A. Kiel, “Tagging Hansenula polymorpha genes by random integration of linear DNA fragments (RALF),” Mol. Genet. Genomics, vol. 266, no. 4, p. 646–656, 2001.
[25] H. Mukaiyama, M. Oku, M. Baba, T. Samizo, A. T. Hammond, B. S. Glick, N. Kato, and Y. Sakai, “Paz2 and 13 other PAZ gene products regulate vacuolar engulfment of peroxisomes during micropexophagy,” Genes Cells, vol. 7, no. 1, p. 75–90, 2002.
[26] W. A. Dunn, J. M. Cregg, J. A. K. W. Kiel, I. J. van der Klei, M. Oku, Y. Sakai, A. A. Sibirny, O. V. Stasyk, and M. Veenhuis, “Pexophagy: the selective autophagy of peroxisomes,” Autophagy, vol. 1, no. 2, p. 75–83, 2005.
[27] Y. Tian, Z. Li, W. Hu, H. Ren, E. Tian, Y. Zhao, Q. Lu, X. Huang, P. Yang, X. Li, X. Wang, A. L. Ková, L. Yu, and H. Zhang, “C. elegans screen identifies autophagy genes specific to multicellular organisms,” Cell, vol. 141, no. 6, p. 1042–1055, 2010.
[28] L. L. Sun, M. Li, F. Suo, X. M. Liu, E. Z. Shen, B. Yang, M. Q. Dong, W. Z. He, and L. L. Du, “Global analysis of fission yeast mating genes reveals new autophagy factors,” PLos. Genet., vol. 9, no. 8, e1003715, 2013.
[29] T. Hara, A. Takamura, C. Kishi, S. Iemura, T. Natsume, J. L. Guan, and N. Mizushima, “FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells,” J. Cell Biol., vol. 181, no. 3, p. 497–510, 2008.
[30] N. Hosokawa, T. Sasaki, S. I. Iemura, T. Natsume, T. Hara, and N. Mizushima, “Atg101, a novel mammalian autophagy protein interacting with Atg13,” Autophagy, vol. 5, no. 7, p. 973–979, 2009.
[31] C. A. Mercer, A. Kaliappan, and P. B. Dennis, “A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy,” Autophagy, vol. 5, no. 5, p. 649–662, 2009.
[32] A. Ropolo, D. Grasso, R. Pardo, M. L. Sacchetti, C. Archange, A. Lo Re, M. Seux, J. Nowak, C. D. Gonzalez, J. L. Iovanna, and M. I. Vaccaro, “The pancreatitis-induced vacuole membrane protein 1 triggers autophagy in mammalian cells,” J. Biol. Chem., vol. 282, no. 51, p. 37124–37133, 2007.
[33] E. Y. Chan, S. Kir, and S. A. Tooze, “siRNA screening of the kinome identifies ULK1 as a multidomain modulator of autophagy,” J. Biol. Chem., vol. 282, no. 35, p. 25464–25474, 2007.
[34] A. Orvedahl, R. Jr. Sumpter, G. Xiao, A. Ng, Z. Zou, Y. Tang, M. Narimatsu, C. Gilpin, Q. Sun, M. Roth, C. V Forst, J. L. Wrana, Y. E. Zhang, K. Luby-Phelps, R. J. Xavier, Y. Xie, and B. Levine, “Image-based genome-wide siRNA screen identifies selective autophagy factors,” Nature, vol. 480, no. 7375, p. 113–117, 2011.
[35] C. M. Hale, Q. Cheng, D. Ortuno, M. Huang, D. Nojima, P. D. Kassner, S. Wang, M. M. Ollmann, and H. J. Carlisle, “Identification of modulators of autophagic flux in an image-based high content siRNA screen,” Autophagy, vol. 12, no. 4, p. 713– 726, 2016.
[36] J. Jung, A. Nayak, V. Schaeffer, T. Starzetz, A. K. Kirsch, S. Müller, I. Dikic, M. Mittelbronn, and C. Behrends, “Multiplex image-based autophagy RNAi screening identifies SMCR8 as ULK1 kinase activity and gene expression regulator,” elife, vol. 6, e23063, 2017.
[37] Y. Ishino, H. Shinagawa, K. Makino, M. Amemura, and A. Nakata, “Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product,” J. Bacteriol., vol. 169, no. 12, p. 5429–5433, 1987.
[38] L. Cong, F. A. Ran, D. Cox, S. Lin, R. Barretto, P. D. Hsu, X. Wu, W. Jiang, L. A. Marraffini, and F. Zhang “Multiplex genome engineering using CRISPR/Cas systems,” Science, vol. 339, no. 6121, p. 819–823, 2013.
[39] P. Mali, L. Yang, K. M. Esvelt, J. Aach, M. Guell, J. E. DiCarlo, J. E. Norville, and G. M. Church, “RNA-guided human genome engineering via Cas9,” Science, vol. 339, no. 6121, p. 823–826, 2013.
[40] M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna, and E. Charpentier, “A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity,” Science, vol. 337, no. 6096, p. 816–821, 2012.
[41] G. Gasiunas, R. Barrangou, P. Horvath, and V. Siksnys, “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria,” Proc. Natl. Acad. Sci., vol. 109, no. 39, p. E2579–E2586, 2012.
[42] R. Böttcher, M. Hollmann, K. Merk, V. Nitschko, C. Obermaier, J. Philippou-Massier, I. Wieland, U. Gaul, and K. Förstemann, “Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells,” Nucleic Acids Res., vol. 42, no. 11, e89, 2014.
[43] S. Kunzelmann, R. Böttcher, I. Schmidts, and K. Förstemann, “A comprehensive toolbox for genome editing in cultured Drosophila melanogaster cells,” G3 (Bethesda), vol. 6, no. 6, p. 1777–1785, 2016.
[44] M. L. Schwartz and E. M. Jorgensen, “SapTrap, a toolkit for high-throughput CRISPR/Cas9 gene modification in Caenorhabditis elegans,” Genetics, vol. 202, no. 4, p. 1277–1288, 2016.
[45] T. Sakuma, S. Nakade, Y. Sakane, K. T. Suzuki, and T. Yamamoto, “MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems,” Nat. Protoc., vol. 11, no. 1, p. 118–133, 2016.
[46] M. Dalvai, J. Loehr, K. Jacquet, C. C. Huard, C. Roques, P. Herst, J. Côté, and Y. Doyon, “A scalable genome-editing-based approach for mapping multiprotein complexes in human cells,” Cell Rep., vol. 13, no. 3, p. 621–633, 2015.
[47] T. Natsume, T. Kiyomitsu, Y. Saga, and M. T. Kanemaki, “Rapid protein depletion in human cells by auxin-inducible degron tagging with short homology donors,” Cell Rep., vol. 15, no. 1, p. 210–218, 2016.
[48] H. Ma, A. Naseri, P. Reyes-Gutierrez, S. A. Wolfe, S. Zhang, and T. Pederson, “Multicolor CRISPR labeling of chromosomal loci in human cells,” Proc. Natl. Acad. Sci., vol. 112, no. 10, p. 3002–3007, 2015.
[49] B. Chen, L. A. Gilbert, B. A. Cimini, J. Schnitzbauer, W. Zhang, G. W. Li, J. Park, E. H. Blackburn, J. S. Weissman, L. S. Qi, and B. Huang, “Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system,” Cell, vol. 155, no. 7, p. 1479–1491, 2013.
[50] P. Mali, J. Aach, P. B. Stranges, K. M. Esvelt, M. Moosburner, S. Kosuri, L. Yang, and G. M. Church, “CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering,” Nat. Biotechnol., vol. 31, no. 9, p. 833–838, 2013.
[51] P. Perez-Pinera, D. D. Kocak, C. M. Vockley, A. F. Adler, A. M. Kabadi, L. R. Polstein, P. I. Thakore, K. A. Glass, D. G. Ousterout, K. W. Leong, F. Guilak, G. E. Crawford, T. E. Reddy, and C. A. Gersbach, “RNA-guided gene activation by CRISPR-Cas9-based transcription factors,” Nat. Methods, vol. 10, no. 10, p. 973–976, 2013.
[52] M. L. Maeder, S. J. Linder, V. M. Cascio, Y. Fu, Q. H. Ho, and J. K. Joung, “CRISPR RNA-guided activation of endogenous human genes,” Nat. Methods, vol. 10, no. 10, p. 977–979, 2013.
[53] S. Konermann, M. D. Brigham, A. Trevino, P. D. Hsu, M. Heidenreich, L. Cong, R. J. Platt, D. A. Scott, G. M. Church, and F. Zhang, “Optical control of mammalian endogenous transcription and epigenetic states,” Nature, vol. 500, no. 7463, p. 472–476, 2013.
[54] L. A. Gilbert, M. H. Larson, L. Morsut, Z. Liu, G. A. Brar, S. E. Torres, N. Stern-Ginossar, O. Brandman, E. H. Whitehead, J. A. Doudna, W. A. Lim, J. S. Weissman, and L. S. Qi, “CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes,” Cell, vol. 154, no. 2, p. 442–451, 2013.
[55] M. Jinek, F. Jiang, D. W. Taylor, S. H. Sternberg, E. Kaya, E. Ma, C. Anders, M. Hauer, K. Zhou, S. Lin, M. Kaplan, A. T. Iavarone, E. Charpentier, E. Nogales, and J. A. Doudna, “Structures of Cas9 endonucleases reveal RNA-mediated conformational activation,” Science, vol. 343, no. 6176, 1247997, 2014.
[56] H. Nishimasu, F. A. Ran, P. D. Hsu, S. Konermann, S. I. Shehata, N. Dohmae, R. Ishitani, F. Zhang, and O. Nureki, “Crystal structure of Cas9 in complex with guide RNA and target DNA,” Cell, vol. 156, no. 5, p. 935–949, 2014.
[57] I. M. Slaymaker, L. Gao, B. Zetsche, D. A. Scott, W. X. Yan, and F. Zhang, “Rationally engineered Cas9 nulceases with improved specificity,” Science, vol. 351, no. 6268, p. 84–88, 2013.
[58] B. Zetsche, J. S. Gootenberg, O. O. Abudayyeh, I. M. Slaymaker, K. S. Makarova, P. Essletzbichler, S. E. Volz, J. Joung, J. van der Oost, A. Regev, E. V. Koonin, and F. Zhang, “Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas System,” Cell, vol. 163, no. 3, p. 759–771, 2015.
[59] O. Shalem, N. E. Sanjana, E. Hartenian, X. Shi, D. A. Scott, T. Mikkelson, D. Heckl, B. L. Ebert, D. E. Root, J. G. Doench, and F. Zhang, “Genome-scale CRISPR-Cas9 knockout screening in human cells,” Science, vol. 343, no. 6166, p. 84– 87, 2014.
[60] T. Wang, J. Wei, D. Sabatini, and E. Lander, “Genetic screens in human cell using the CRISPR/Cas9 system,” Science, vol. 343, no. 6166, p. 80–84, 2014.
[61] I. Aladzsity, M. L. Tóth, T. Sigmond, E. Szabó, B. Bicsák, J. Barna, Á. Regos, L. Orosz, A. L. Kovács, and T. Vellai, “Autophagy genes unc-51 and bec-1 are required for normal cell size in Caenorhabditis elegans,” Genetics, vol. 177, no. 1, p. 655–660, 2007.
[62] K. Takacs-Vellai, T. Vellai, A. Puoti, M. Passannante, C. Wicky, A. Streit, A. L. Kovacs, and F. Müller, “Inactivation of the autophagy gene bec-1 triggers apoptotic cell death in C. elegans,” Curr. Biol., vol. 15, no. 16, p. 1513–1517, 2005.
[63] T. Yamada T, A. R. Carson, I. Caniggia, K. Umebayashi, T. Yoshimori, K. Nakabayashi, S. W. Scherer, “Endothelial nitric-oxide synthase antisense (NOS3AS) gene encodes an autophagy-related protein (APG9-like2) highly expressed in trophoblast,” J. Biol. Chem.,vol. 280, no. 18, p. 18283-18290, 2005.
[64] F. Li, T. Chung, and R. D. Vierstra, “AUTOPHAGY-RELATED11 plays a critical role in general autophagy- and senescence-induced mitophagy in Arabidopsis,” Plant Cell, vol. 26, no. 2, p. 788–807, 2014.
[65] E. S. Hars, H. Qi, A. G. Ryazanov, S. Jin, L. Cai, C. Hu, and L. F. Liu, “Autophagy regulates ageing in C. elegans,” Autophagy, vol. 3, no. 2, p. 93–95, 2007.
[66] D. Zhao, X. M. Liu, Z. Q. Yu, L. L. Sun, X. Xiong, M. Q. Dong, and L. L. Du, “Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast,” J. Cell Sci., vol. 129, no. 22, p. 4289–4304, 2016.
[67] K. Okamoto, N. Kondo-Okamoto, and Y. Ohsumi, “Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy,” Dev. Cell, vol. 17, no. 1, p. 87–97, 2009.
[68] T. Kanki, K. Wang, M. Baba, C. R. Bartholomew, M. A. Lynch-Day, Z. Du, J. Geng, K. Mao, Z. Yang, W. L. Yen, and D. J. Klionsky, “A genomic screen for yeast mutants defective in selective mitochondria autophagy,” Mol. Biol. Cell, vol. 20, no. 22, p. 4730–4738, 2009.
[69] K. Suzuki, C. Kondo, M. Morimoto, and Y. Ohsumi, “Selective transport of α-mannosidase by autophagic pathways: identification of a novel receptor, Atg34p,” J. Biol. Chem., vol. 285, no. 39, p. 30019–30025, 2010.
[70] V. Y. Nazarko, T. Y. Nazarko, J. C. Farré, O. V. Stasyk, D. Warnecke, S. Ulaszewski, J. M. Cregg, A. A. Sibirny, and S. Subramani, “Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris,” Autophagy, vol. 7, no. 4, p. 375–385, 2011.
[71] A. M. Motley, J. M. Nuttall, and E. H. Hettema, “Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae,” EMBO J., vol. 31, no. 13, p. 2852–2868, 2012.
[72] T. Y. Nazarko, K. Ozeki, A. Till, G. Ramakrishnan, P. Lotfi, M. Yan, and S. Subramani, “Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy,” J. Cell Biol., vol. 204, no. 4, p. 541–557, 2014.
[73] Y. Araki, W. C. Ku, M. Akioka, A. I. May, Y. Hayashi, F. Arisaka, Y. Ishihama, and Y. Ohsumi, “Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity,” J. Cell Biol., vol. 203, no. 2, p. 299–313, 2013.
[74] Y. Ohashi, N. Soler, M. García Ortegón, L. Zhang, M. L. Kirsten, O. Perisic, G. R. Masson, J. E. Burke, A. J. Jakobi, A. A. Apostolakis, C. M. Johnson, M. Ohashi, N. T. Ktistakis, C. Sachse, R. L. Williams, “Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex,” Autophagy, vol. 12, no. 11, p. 2129-2144, 2016.
[75] K. Mochida, Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and H. Nakatogawa, “Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus,” Nature, vol. 522, no. 7556, p. 359–362, 2015.
[76] Z. Yao, E. Delorme-Axford, S. K. Backues, and D. J. Klionsky, “Atg41/Icy2 regulates autophagosome formation,” Autophagy, vol. 11, no. 12, p. 2288–2299, 2015.
[77] K. R. Parzych, A. Ariosa, M. Mari, and D. J. Klionsky, “A newly characterized vacuolar serine carboxypeptidase, Atg42/Ybr139w, is required for normal vacuole function and the terminal steps of autophagy in the yeast Saccharomyces cerevisiae,” Mol. Biol. Cell, vol. 29, no. 9, p. 1089–1099, 2018.
[78] D. J. Klionsky, J. M. Cregg, W. A. Jr. Dunn, S. D. Emr, Y. Sakai, I. V. Sandoval, A. Sibirny, S. Subramani, M. Thumm, M. Veenhuis, and Y. Ohsumi, “A unified nomenclature for yeast autophagy-related genes,” vol. 5, no. 4, p. 539–545, 2003.
[79] H. Nakatogawa, K. Suzuki, Y. Kamada, and Y. Ohsumi, “Dynamics and diversity in autophagy mechanisms: lessons from yeast,” Nat. Rev. Mol. Cell Biol., vol. 10, no. 7, p. 458–467, 2009.
[80] N. Mizushima, T. Yoshimori, and Y. Ohsumi, “The role of Atg proteins in autophagosome formation,” Annu. Rev. Cell Dev. Biol., vol. 27, no. 1, p. 107–132, 2011.
[81] N. T. Ktistakis and S. A. Tooze, “Digesting the expanding mechanisms of autophagy,” Trends Cell Biol., vol. 26, no. 8, p. 624–635, 2016.
[82] T. Wang, K. Birsoy, N. W. Hughes, K. M. Krupczak, Y. Post, J. J. Wei, E. S. Lander, and D. M. Sabatini, “Identification and characterization of essential genes in the human genome,” Science, vol. 350, no. 6264, p. 1096–1101, 2015.
[83] V. A. Blomen, P. Májek, L. T. Jae, J. W. Bigenzahn, J. Nieuwenhuis, J. Starling, R. Sacco, F. R. van Diemen, N. Olk, A. Stukalov, C. Marceau, H. Janssen, J. E. Carette, K. L. Bennett, J. Colinge, G. Superti-Furga, and T. R. Brummelkamp, “Gene essentiality and synthetic lethality in haploid human cells,” Science, vol. 350, no. 6264, p. 1092–1096, 2015.
[84] H. Ma, Y. Dang, Y. Wu, G. Jia, E. Anaya, J. Zhang, S. Abraham, J. G. Choi, G. Shi, N. Manjunath, and H. Wu, “A CRISPR-based screen identifies genes essential for West-Nile-Virus-induced cell death,” Cell Rep., vol. 12, no. 4, p. 673–683, 2015.
[85] C. D. Marceau, A. S. Puschnik, K. Majzoub, Y. S. Ooi, S. M. Brewer, G. Fuchs, K. Swaminathan, M. A. Mata, J. E. Elias, P. Sarnow, and J. E. Carette, “Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens,” Nature, vol. 535, no. 7610, p. 159–163, 2016.
[86] R. Dejesus, F. Moretti, G. McAllister, Z. Wang, P. Bergman, S. Liu, E. Frias, J. Alford, J. S. Reece-Hoyes, A. Lindeman, J. Kelliher, C. Russ, J. Knehr, W. Carbone, M. Beibel, G. Roma, A. Ng, J. A. Tallarico, J. A. Porter, R. J. Xavier, C. Mickanin, L. O. Murphy, G. R. Hoffman, and B. Nyfeler, “Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62,” elife, vol. 5, e17290, 2016.
[87] J. M. Goodwin, W. E. Dowdle, R. DeJesus, Z. Wang, P. Bergman, M. Kobylarz, A. Lindeman, R. J. Xavier, G. McAllister, B. Nyfeler, G. Hoffman, and L. O. Murphy, “Autophagy-independent lysosomal targeting regulated by ULK1/2-FIP200 and ATG9,” Cell Rep., vol. 20, no. 10, p. 2341–2356, 2017.
[88] Y. Katsuragi, Y. Ichimura, and M. Komatsu, “Regulation of the Keap1–Nrf2 pathway by p62/SQSTM1,” Curr. Opin. Toxicol., vol. 1, p. 54–61, 2016.
[89] M. H. Sahani, E. Itakura, and N. Mizushima, “Expression of the autophagy substrate SQSTM1/p62 is restored during prolonged starvation depending on transcriptional upregulation and autophagy-derived amino acids,” Autophagy, vol. 10, no. 3, p. 431–441, 2014.
[90] W. E. Dowdle, B. Nyfeler, J. Nagel, R. A. Elling, S. Liu, E. Triantafellow, S. Menon, Z. Wang, A. Honda, G. Pardee, J. Cantwell, C. Luu, I. Cornella-Taracido, E. Harrington, P. Fekkes, H. Lei, Q. Fang, M. E. Digan, D. Burdick, A. F. Powers, S. B. Helliwell, S. Daquin, J. Bastien, H. Wang, D. Wiederschain, J. Kuerth, P. Bergman, D. Schwalb, J. Thomas, S. Ugwonali, F. Harbinski, J. Tallarico, C. J. Wilson, V. E. Myer, J. A. Porter, D. E. Bussiere, P. M. Finan, M. A. Labow, X. Mao, L. G. Hamann, B. D. Manning, R. A. Valdez, T. Nicholson, M. Schirle, M. S. Knapp, E. P. Keaney, and L. O. Murphy, “Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo,” Nat. Cell Biol., vol. 16, no. 11, p. 1069–1079, 2014.
[91] J. D. Mancias, X. Wang, S. P. Gygi, J. W. Harper, and A. C. Kimmelman, “Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy,” Nature, vol. 509, no. 7498, p. 105–109, 2014.
[92] K. Morita, Y. Hama, T. Izume, N. Tamura, T. Ueno, Y. Yamashita, Y. Sakamaki, K. Mimura, H. Morishita, W. Shihoya, O. Nureki, H. Mano, and N. Mizushima, “Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation,” J. Cell Biol., vol. 217, no. 11, p. 3817-3828, 2018.
[93] T. Kaizuka, H. Morishita, Y. Hama, S. Tsukamoto, T. Matsui, Y. Toyota, A. Kodama, T. Ishihara, T. Mizushima, and N. Mizushima, “An autophagic flux probe that releases an internal control,” Mol. Cell, vol. 64, no. 4, p. 835–849, 2016.
[94] E. Shvets, E. Fass, and Z. Elazar, “Utilizing flow cytometry to monitor autophagy in living mammalian cells,” Autophagy, vol. 4, no. 5, p. 621–628, 2008.
[95] K. B. Larsen, T. Lamark, A. Øvervatn, I. Harneshaug, T. Johansen, and G. Bjørkøy, “A reporter cell system to monitor autophagy based on p62/SQSTM1,” Autophagy, vol. 6, no. 6, p. 784–793, 2010.
[96] N. Hosokawa, Y. Hara, and N. Mizushima, “Generation of cell lines with tetracycline-regulated autophagy and a role for autophagy in controlling cell size,” FEBS Lett., vol. 580, no. 15, p. 2623–2629, 2006.
[97] T. Kitamura, Y. Koshino, F. Shibata, T. Oki, H. Nakajima, T. Nosaka, and H. Kumagai, “Retrovirus-mediated gene transfer and expression cloning: powerful tools in functional genomics,” Exp Hematol, vol. 31, no. 11, p. 1007–1014, 2003.
[98] T. Nishimura, N. Tamura, N. Kono, Y. Shimanaka, H. Arai, H. Yamamoto, and N. Mizushima, “Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains,” EMBO J., vol. 36, no. 12, p. 1719–1735, 2017.
[99] E. Itakura and N. Mizushima, “Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins,” Autophagy, vol. 6, no. 6, p. 764–776, 2010.
[100] M. N. Itakura E, Kishi C, Inoue K, and N. Mizushima, “Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG,” Mol. Biol. Cell, vol. 19, no. 12, p. 5360–5372, 2008.
[101] T. Saitoh, H. Nakano, N. Yamamoto, and S. Yamaoka, “Lymphotoxin-β receptor mediates NEMO-independent NF-κB activation,” FEBS Lett., vol. 532, no. 1-2, p. 45–51, 2002.
[102] Y. Kabeya, N. Mizushima, T. Ueno, A. Yamamoto, T. Kirisako, T. Noda, E. Kominami, Y. Ohsumi, and T. Yoshimori, “LC3, a mammalian homolog of yeast Apg8p, is localized in autophagosome membranes after processing,” EMBO J., vol. 19, no. 21, p. 5720-5728, 2000.
[103] J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J. Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods, vol. 9, no. 7, p. 676–682, 2012.
[104] S. Kumar, G. Stecher, M. Li, C. Knyaz, and K. Tamura, “MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms,” Mol. Biol. Evol., vol. 35, no. 6, p. 1547–1549, 2018.
[105] N. E. Sanjana, O. Shalem, and F. Zhang, “Improved vectors and genome-wide libraries for CRISPR screening,” Nat. Methods, vol. 11, no. 8, p. 783–784, 2014.
[106] K. G. Bache, T. Slagsvold, A. Cabezas, K. R. Rosendal, C. Raiborg, and H. Stenmark “The growth-regulatory protein HCRP1/hVps37A is a subunit of mammalian ESCRT-I and mediates receptor down-regulation,” Mol. Biol. Cell, vol. 15, no. 9, p. 4337–4336, 2004.
[107] L. Christ, C. Raiborg, E. M. Wenzel, C. Campsteijn, and H. Stenmark, “Cellular functions and molecular mechanisms of the ESCRT membrane-scission machinery,” Trends Biochem. Sci., vol. 42, no. 1, p. 42–56, 2016.
[108] T. E. Rusten and H. Stenmark, “How do ESCRT proteins control autophagy?” J. Cell Sci., vol. 122, no. Pt 13, p. 2179–2183, 2009.
[109] F. Lotti, W. L. Imlach, L. Saieva, E. S. Beck, L. T. Hao, D. K. Li, W. Jiao, G. Z. Mentis, C. E. Beattie, B. D. McCabe, L. Pellizzoni, “An SMN-dependent U12 splicing event essential for motor circuit function,” Cell, vol. 151, no. 2, p. 440–454, 2012.
[110] R. D. Finn, P. Coggill, R. Y. Eberhardt, S. R. Eddy, J. Mistry, A. L. Mitchell, S. C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G. A. Salazar, J. Tate, and A. Bateman, “The Pfam protein families database: towards a more sustainable future,” Nucleic Acids Res., vol. 44, no. D1, p. D279–D285, 2016.
[111] W. T. Doerrler, R. Sikdar, S. Kumar, and L. A. Boughner, “New functions for the ancient DedA membrane protein family,” J. Bacteriol., vol. 195, no. 1, p. 3–11, 2013.
[112] A. Krogh, B. Larsson, G. von Heijne, and E. L. Sonnhammer, “Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes,” J. Mol. Biol., vol. 305, no. 3, p. 567–580, 2001.
[113] G. E. Tusnády and I. Simon, “The HMMTOP transmembrane topology prediction server,” Bioinformatics, vol. 17, no. 9, p. 849–850, 2001.
[114] Y. G. Zhao, Y. Chen, G. Miao, H. Zhao, W. Qu, D. Li, Z. Wang, N. Liu, L. Li, S. Chen, P. Liu, D. Feng, and H. Zhang, “The ER-localized transmembrane protein EPG-3/VMP1 regulates SERCA activity to control ER-isolation membrane contacts for autophagosome formation,” Mol. Cell, vol. 67, no. 6, p. 974–989.e6, 2017.
[115] K. Khafizov, R. Staritzbichler, M. Stamm, and L. R. Forrest, “A study of the evolution of inverted-topology repeats from LeuT-fold transporters using AlignMe,” Biochemistry, vol. 49, no. 50, p. 10702–10713, 2010.
[116] R. Keller, C. Ziegler, and D. Schneider, “When two turn into one: evolution of membrane transporters from half modules,” Biol. Chem., vol. 395, no. 12, p. 1379–1388, 2014.
[117] Y. Ichimura, S. Waguri, Y. shin Sou, S. Kageyama, J. Hasegawa, R. Ishimura, T. Saito, Y. Yang, T. Kouno, T. Fukutomi, T. Hoshii, A. Hirao, K. Takagi, T. Mizushima, H. Motohashi, M. S. Lee, T. Yoshimori, K. Tanaka, M. Yamamoto, and M. Komatsu, “Phosphorylation of p62 Activates the Keap1-Nrf2 pathway during selective autophagy,” Mol. Cell, vol. 51, no. 5, p. 618–631, 2013.
[118] C. Kishi-Itakura, I. Koyama-Honda, E. Itakura, and N. Mizushima, “Ultrastructural analysis of autophagosome organization using mammalian autophagy-deficient cells,” J. Cell Sci., vol. 127, no. 18, p. 4089-4102, 2014.
[119] L. C. Tábara and R. Escalante, “VMP1 establishes ER-microdomains that regulate membrane contact sites and autophagy,” PLoS One, vol. 11, no. 11, e0166499, 2016.
[120] F. Moretti, P. Bergman, S. Dodgson, D. Marcellin, I. Claerr, J. M. Goodwin, R. DeJesus, Z. Kang, C. Antczak, D. Begue, D. Bonenfant, A. Graff, C. Genoud, J. S. Reece-Hoyes, C. Russ, Z. Yang, G. R. Hoffman, M. Mueller, L. O. Murphy, R. J. Xavier, B. Nyfeler, “TMEM41B is a novel regulator of autophagy and lipid mobilization,” EMBO Rep, vol. 9, no. 19, e45889, 2018
[121] C. J. Shoemaker, T. Q. Huang, N. R. Weir, N. Polyakov, V. Denic, “A CRISPR screening approach for identifying novel autophagy-related factors and cytoplasm-to-lysosome trafficking routes,” bioRχiv, doi.org/10.1101/229732, 2017
[122] L. A. Gilbert, M. A. Horlbeck, B. Adamson, J. E. Villalta, Y. Chen, E. H. Whitehead, C. Guimaraes, B. Panning, H. L. Ploegh, M. C. Bassik, L. S. Qi, M. Kampmann, and J. S. Weissman, “Genome-scale CRISPR-mediated control of gene repression and activation,” Cell, vol. 159, no. 3, p. 647–661, 2014.
[123] M. Costanzo, B. VanderSluis, E. N. Koch, A. Baryshnikova, C. Pons, G. Tan, W. Wang, M. Usaj, J. Hanchard, S. D. Lee, V. Pelechano, E. B. Styles, M. Billmann, J. van Leeuwen, N. van Dyk, Z. Y. Lin, E. Kuzmin, J. Nelson, J. S. Piotrowski, T. Srikumar, S. Bahr, Y. Chen, R. Deshpande, C. F. Kurat, S. C. Li, Z. Li, M. M. Usaj, H. Okada, N. Pascoe, B. J. S. Luis, S. Sharifpoor, E. Shuteriqi, S. W. Simpkins, J. Snider, H. G. Suresh, Y. Tan, H. Zhu, N. Malod-Dognin, V. Janjic, N. Przulj, O. G. Troyanskaya, I. Stagljar, T. Xia, Y. Ohya, A. C. Gingras, B. Raught, M. Boutros, L. M. Steinmetz, C. L. Moore, A. P. Rosebrock, A. A. Caudy, C. L. Myers, B. Andrews, and C. Boone, “A global genetic interaction network maps a wiring diagram of cellular function,” Science, vol. 353, no. 6306, aaf1420, 2016.
[124] E. Kuzmin, B. VanderSluis, W. Wang, G. Tan, R. Deshpande, Y. Chen, M. Usaj, A. Balint, M. M. Usaj, J. van Leeuwen, E. N. Koch, C. Pons, A. J. Dagilis, M. Pryszlak, J. Z. Y. Wang, J. Hanchard, M. Riggi, K. Xu, H. Heydari, B. J. S. Luis, E. Shuteriqi, H. Zhu, N. van Dyk, S. Sharifpoor, M. Costanzo, R. Loewith, A. Caudy, D. Bolnick, G. W. Brown, B. J. Andrews, C. Boone, and C. L. Myers, “Systematic analysis of complex genetic interactions,” Science, vol. 360, no. 6386, p. eaao1729, 2018.
[125] W. A. Dunn, “Studies on the mechanisms of autophagy: formation of the vacuole,” J. Cell Biol., vol. 110, no. 6, p. 1923–1933, 1990.
[126] K. Morita, Y. Hama, and N. Mizushima, “TMEM41B functions with VMP1 in autophagosome formation,” Autophagy., [Epub ahead of print], 2019
論文の公開元へ
