Acknowledgement
This study was supported by grants from the Basic Science Research Program through the NRF (NRF-2020R1A2C3004973), NRF (NRF-2018R1A5A2023127), and the BK21 FOUR program through the National Research Foundation (NRF) of Korea funded by the Ministry of Education (MOE, Korea).
References
- Axe, E. L., Walker, S. A., Manifava, M., Chandra, P., Roderick, H. L., Habermann, A., Griffiths, G. and Ktistakis, N. T. (2008) Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J. Cell Biol. 182, 685-701.
- Backer, J. M. (2016) The intricate regulation and complex functions of the Class III phosphoinositide 3-kinase Vps34. Biochem. J. 473, 2251-2271.
- Bago, R., Malik, N., Munson, M. J., Prescott, A. R., Davies, P., Sommer, E., Shpiro, N., Ward, R., Cross, D., Ganley, I. G. and Alessi, D. R. (2014) Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase. Biochem. J. 463, 413-427.
- Banta, L. M., Robinson, J. S., Klionsky, D. J. and Emr, S. D. (1988) Organelle assembly in yeast: characterization of yeast mutants defective in vacuolar biogenesis and protein sorting. J. Cell Biol. 107, 1369-1383.
- Baskaran, S., Carlson, L. A., Stjepanovic, G., Young, L. N., Kim, D. J., Grob, P., Stanley, R. E., Nogales, E. and Hurley, J. H. (2014) Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex. Elife 3, e05115.
- Baskaran, S., Ragusa, M. J. and Hurley, J. H. (2012) How Atg18 and the WIPIs sense phosphatidylinositol 3-phosphate. Autophagy 8, 1851-1852.
- Bertovic, I., Kurelic, R., Milosevic, I., Bender, M., Krauss, M., Haucke, V. and Jurak Begonja, A. (2020) Vps34 derived phosphatidylinositol 3-monophosphate modulates megakaryocyte maturation and proplatelet production through late endosomes/lysosomes. J. Thromb. Haemost. 18, 1756-1772.
- Bilanges, B., Alliouachene, S., Pearce, W., Morelli, D., Szabadkai, G., Chung, Y. L., Chicanne, G., Valet, C., Hill, J. M., Voshol, P. J., Collinson, L., Peddie, C., Ali, K., Ghazaly, E., Rajeeve, V., Trichas, G., Srinivas, S., Chaussade, C., Salamon, R. S., Backer, J. M., Scudamore, C. L., Whitehead, M. A., Keaney, E. P., Murphy, L. O., Semple, R. K., Payrastre, B., Tooze, S. A. and Vanhaesebroeck, B. (2017) Vps34 PI 3-kinase inactivation enhances insulin sensitivity through reprogramming of mitochondrial metabolism. Nat. Commun. 8, 1804.
- Burda, P., Padilla, S. M., Sarkar, S. and Emr, S. D. (2002) Retromer function in endosome-to-Golgi retrograde transport is regulated by the yeast Vps34 PtdIns 3-kinase. J. Cell Sci. 115, 3889-3900.
- Chavez-Dominguez, R., Perez-Medina, M., Lopez-Gonzalez, J. S., Galicia-Velasco, M. and Aguilar-Cazares, D. (2020) The double-edge sword of autophagy in cancer: from tumor suppression to protumor activity. Front. Oncol. 10, 578418.
- Chen, M., Ren, X., Nguyen, T. N., Khuu, G., Cook, A. S. I., Lazarou, M. and Hurley, J. H. (2024) Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex. Biophys. J. 123, 345A.
- Di Donato, M., Giovannelli, P., Migliaccio, A. and Bilancio, A. (2022) Inhibition of Vps34 and p110delta PI3K impairs migration, invasion and three-dimensional spheroid growth in breast cancer cells. Int. J. Mol. Sci. 23, 9008.
- Dooley, H. C., Razi, M., Polson, H. E., Girardin, S. E., Wilson, M. I. and Tooze, S. A. (2014) WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol. Cell 55, 238-252.
- Dowdle, W. E., Nyfeler, B., Nagel, J., Elling, R. A., Liu, S., Triantafellow, E., Menon, S., Wang, Z., Honda, A., Pardee, G., Cantwell, J., Luu, C., Cornella-Taracido, I., Harrington, E., Fekkes, P., Lei, H., Fang, Q., Digan, M. E., Burdick, D., Powers, A. F., Helliwell, S. B., D'Aquin, S., Bastien, J., Wang, H., Wiederschain, D., Kuerth, J., Bergman, P., Schwalb, D., Thomas, J., Ugwonali, S., Harbinski, F., Tallarico, J., Wilson, C. J., Myer, V. E., Porter, J. A., Bussiere, D. E., Finan, P. M., Labow, M. A., Mao, X., Hamann, L. G., Manning, B. D., Valdez, R. A., Nicholson, T., Schirle, M., Knapp, M. S., Keaney, E. P. and Murphy, L. O. (2014) Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo. Nat. Cell Biol. 16, 1069-1079.
- Dyczynski, M., Yu, Y., Otrocka, M., Parpal, S., Braga, T., Henley, A. B., Zazzi, H., Lerner, M., Wennerberg, K., Viklund, J., Martinsson, J., Grander, D., De Milito, A. and Pokrovskaja Tamm, K. (2018) Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib. Cancer Lett. 435, 32-43.
- Egan, D. F., Chun, M. G., Vamos, M., Zou, H., Rong, J., Miller, C. J., Lou, H. J., Raveendra-Panickar, D., Yang, C. C., Sheffler, D. J., Teriete, P., Asara, J. M., Turk, B. E., Cosford, N. D. and Shaw, R. J. (2015) Small molecule inhibition of the autophagy kinase ULK1 and identification of ULK1 substrates. Mol. Cell 59, 285-297.
- Fan, W., Nassiri, A. and Zhong, Q. (2011) Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L). Proc. Natl. Acad. Sci. U. S. A. 108, 7769-7774.
- Furuya, T., Kim, M., Lipinski, M., Li, J., Kim, D., Lu, T., Shen, Y., Rameh, L., Yankner, B., Tsai, L. H. and Yuan, J. (2010) Negative regulation of Vps34 by Cdk mediated phosphorylation. Mol. Cell 38, 500-511.
- Gatica, D., Wen, X., Cheong, H. and Klionsky, D. J. (2021) Vac8 determines phagophore assembly site vacuolar localization during nitrogen starvation-induced autophagy. Autophagy 17, 1636-1648.
- Giridharan, S. S. P., Luo, G., Rivero-Rios, P., Steinfeld, N., Tronchere, H., Singla, A., Burstein, E., Billadeau, D. D., Sutton, M. A. and Weisman, L. S. (2022) Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate retriever-mediated recycling on endosomes. Elife 11, e69709.
- Herman, P. K., Stack, J. H., DeModena, J. A. and Emr, S. D. (1991) A novel protein kinase homolog essential for protein sorting to the yeast lysosome-like vacuole. Cell 64, 425-437.
- Hill, S. M., Wrobel, L. and Rubinsztein, D. C. (2019) Post-translational modifications of Beclin 1 provide multiple strategies for autophagy regulation. Cell Death Differ. 26, 617-629.
- Hitomi, K., Kotani, T., Noda, N. N., Kimura, Y. and Nakatogawa, H. (2023) The Atg1 complex, Atg9, and Vac8 recruit PI3K complex I to the pre-autophagosomal structure. J. Cell Biol. 222, e202210017.
- Hu, Z., Luo, Y., Liu, Y., Luo, Y., Wang, L., Gou, S., Peng, Y., Wei, R., Jia, D., Wang, Y., Gao, S. and Zhang, Y. (2023) Partial inhibition of class III PI3K VPS-34 ameliorates motor aging and prolongs health span. PLoS Biol. 21, e3002165.
- Hu, Z., Raucci, S., Jaquenoud, M., Hatakeyama, R., Stumpe, M., Rohr, R., Reggiori, F., De Virgilio, C. and Dengjel, J. (2019) Multilayered control of protein turnover by TORC1 and Atg1. Cell Rep. 28, 3486-3496.
- Itakura, E., Kishi, C., Inoue, K. and Mizushima, N. (2008) Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol. Biol. Cell 19, 5360-5372.
- Itakura, E. and Mizushima, N. (2010) Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy 6, 764-776.
- Jaber, N., Dou, Z., Chen, J. S., Catanzaro, J., Jiang, Y. P., Ballou, L. M., Selinger, E., Ouyang, X., Lin, R. Z., Zhang, J. and Zong, W. X. (2012) Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function. Proc. Natl. Acad. Sci. U. S. A. 109, 2003-2008.
- Jaber, N., Mohd-Naim, N., Wang, Z., DeLeon, J. L., Kim, S., Zhong, H., Sheshadri, N., Dou, Z., Edinger, A. L., Du, G., Braga, V. M. and Zong, W. X. (2016) Vps34 regulates Rab7 and late endocytic trafficking through recruitment of the GTPase-activating protein Armus. J. Cell Sci. 129, 4424-4435.
- Jaber, N. and Zong, W. X. (2013) Class III PI3K Vps34: essential roles in autophagy, endocytosis, and heart and liver function. Ann. N. Y. Acad. Sci. 1280, 48-51.
- Jao, C. C., Ragusa, M. J., Stanley, R. E. and Hurley, J. H. (2013) A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. Proc. Natl. Acad. Sci. U. S. A. 110, 5486-5491.
- Jia, M., Yue, X., Sun, W., Zhou, Q., Chang, C., Gong, W., Feng, J., Li, X., Zhan, R., Mo, K., Zhang, L., Qian, Y., Sun, Y., Wang, A., Zou, Y., Chen, W., Li, Y., Huang, L., Yang, Y., Zhao, Y. and Cheng, X. (2023) ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation. Sci. Adv. 9, eadg4993.
- Jiang, X., Bao, Y., Liu, H., Kou, X., Zhang, Z., Sun, F., Qian, Z., Lin, Z., Li, X., Liu, X., Jiang, L. and Yang, Y. (2017) VPS34 stimulation of p62 phosphorylation for cancer progression. Oncogene 36, 6850-6862.
- Jo, S. B., Sung, S. J., Choi, H. S., Park, J. S., Hong, Y. K. and Joe, Y. A. (2022) Modulation of autophagy is a potential strategy for enhancing the anti-tumor effect of mebendazole in glioblastoma cells. Biomol. Ther. (Seoul) 30, 616-624.
- Katzmann, D. J., Stefan, C. J., Babst, M. and Emr, S. D. (2003) Vps27 recruits ESCRT machinery to endosomes during MVB sorting. J. Cell Biol. 162, 413-423.
- Kihara, A., Noda, T., Ishihara, N. and Ohsumi, Y. (2001) Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J. Cell Biol. 152, 519-530.
- Kim, B. W., Jin, Y., Kim, J., Kim, J. H., Jung, J., Kang, S., Kim, I. Y., Kim, J., Cheong, H. and Song, H. K. (2018) The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation. Autophagy 14, 2104-2116.
- Kim, H. J., Zhong, Q., Sheng, Z. H., Yoshimori, T., Liang, C. and Jung, J. U. (2012) Beclin-1-interacting autophagy protein Atg14L targets the SNARE-associated protein Snapin to coordinate endocytic trafficking. J. Cell Sci. 125, 4740-4750.
- Kim, J., Kim, Y. C., Fang, C., Russell, R. C., Kim, J. H., Fan, W., Liu, R., Zhong, Q. and Guan, K. L. (2013) Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 152, 290-303.
- Kobylarz, M. J., Goodwin, J. M., Kang, Z. B., Annand, J. W., Hevi, S., O'Mahony, E., McAllister, G., Reece-Hoyes, J., Wang, Q., Alford, J., Russ, C., Lindeman, A., Beibel, M., Roma, G., Carbone, W., Knehr, J., Loureiro, J., Antczak, C., Wiederschain, D., Murphy, L. O., Menon, S. and Nyfeler, B. (2020) An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells. PLoS One 15, e0235551.
- Lee, M. J., Park, J. S., Jo, S. B. and Joe, Y. A. (2023a) Enhancing anti-cancer therapy with selective autophagy inhibitors by targeting protective autophagy. Biomol. Ther. (Seoul) 31, 1-15.
- Lee, Y., Kim, B., Jang, H. S. and Huh, W. K. (2023b) Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae. Autophagy 19, 2428-2442
- Li, X. L., Zhou, J., Xia, C. J., Min, H., Lu, Z. K. and Chen, Z. R. (2021) PRIMA-1(met) induces autophagy in colorectal cancer cells through upregulation of the mTOR/AMPK-ULK1-Vps34 signaling cascade. Oncol. Rep. 45, 86.
- Li, Y. and Chen, Y. (2019) AMPK and autophagy. In Autophagy: Biology and Diseases: Basic Science (Z.-H. Qin, Ed.), pp. 85-108. Springer, Singapore.
- Liang, C., Lee, J. S., Inn, K. S., Gack, M. U., Li, Q., Roberts, E. A., Vergne, I., Deretic, V., Feng, P., Akazawa, C. and Jung, J. U. (2008) Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat. Cell Biol. 10, 776-787.
- Liu, Y., Hu, M., Luo, D., Yue, M., Wang, S., Chen, X., Zhou, Y., Wang, Y., Cai, Y., Hu, X., Ke, Y., Yang, Z. and Hu, H. (2017) Class III PI3K positively regulates platelet activation and thrombosis via PI(3)P-directed function of NADPH oxidase. Arterioscler. Thromb. Vasc. Biol. 37, 2075-2086.
- Liu, Y., Yang, Q., Chen, S., Li, Z. and Fu, L. (2023) Targeting VPS34 in autophagy: an update on pharmacological small-molecule compounds. Eur. J. Med. Chem. 256, 115467.
- Lu, J., He, L., Behrends, C., Araki, M., Araki, K., Jun Wang, Q., Catanzaro, J. M., Friedman, S. L., Zong, W. X., Fiel, M. I., Li, M. and Yue, Z. (2014) NRBF2 regulates autophagy and prevents liver injury by modulating Atg14L-linked phosphatidylinositol-3 kinase III activity. Nat. Commun. 5, 3920.
- Ma, M., Liu, J. J., Li, Y., Huang, Y., Ta, N., Chen, Y., Fu, H., Ye, M. D., Ding, Y., Huang, W., Wang, J., Dong, M. Q., Yu, L. and Wang, H. W. (2017a) Cryo-EM structure and biochemical analysis reveal the basis of the functional difference between human PI3KC3-C1 and -C2. Cell Res. 27, 989-1001.
- Ma, X., Zhang, S., He, L., Rong, Y., Brier, L. W., Sun, Q., Liu, R., Fan, W., Chen, S., Yue, Z., Kim, J., Guan, K. L., Li, D. and Zhong, Q. (2017b) MTORC1-mediated NRBF2 phosphorylation functions as a switch for the class III PtdIns3K and autophagy. Autophagy 13, 592-607.
- Maeda, S., Otomo, C. and Otomo, T. (2019) The autophagic membrane tether ATG2A transfers lipids between membranes. Elife 8, e45777.
- Matsunaga, K., Saitoh, T., Tabata, K., Omori, H., Satoh, T., Kurotori, N., Maejima, I., Shirahama-Noda, K., Ichimura, T., Isobe, T., Akira, S., Noda, T. and Yoshimori, T. (2009) Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat. Cell Biol. 11, 385-396.
- Meijer, A. J. and Klionsky, D. J. (2011) Vps34 is a phosphatidylinositol 3-kinase, not a phosphoinositide 3-kinase. Autophagy 7, 563-564.
- Menon, M. B. and Dhamija, S. (2018) Beclin 1 phosphorylation - at the center of autophagy regulation. Front. Cell Dev. Biol. 6, 137.
- Mercer, T. J., Ohashi, Y., Boeing, S., Jefferies, H. B. J., De Tito, S., Flynn, H., Tremel, S., Zhang, W., Wirth, M., Frith, D., Snijders, A. P., Williams, R. L. and Tooze, S. A. (2021) Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK/VPS34 interplay in the regulation of autophagy. EMBO J. 40, e105985.
- Murali, P., Verma, K., Rungrotmongkol, T., Thangavelu, P. and Karuppasamy, R. (2021) Targeting the autophagy specific lipid kinase VPS34 for cancer treatment: an integrative repurposing strategy. Protein J. 40, 41-53.
- Murray, J. T., Panaretou, C., Stenmark, H., Miaczynska, M. and Backer, J. M. (2002) Role of Rab5 in the recruitment of hVps34/p150 to the early endosome. Traffic 3, 416-427.
- Nguyen, A., Lugarini, F., David, C., Hosnani, P., Alagoz, C., Friedrich, A., Schlutermann, D., Knotkova, B., Patel, A., Parfentev, I., Urlaub, H., Meinecke, M., Stork, B. and Faesen, A. C. (2023a) Metamorphic proteins at the basis of human autophagy initiation and lipid transfer. Mol. Cell 83, 2077-2090.
- Nguyen, T. H., Nguyen, T. M., Ngoc, D. T. M., You, T., Park, M. K. and Lee, C. H. (2023b) Unraveling the Janus-faced role of autophagy in hepatocellular carcinoma: implications for therapeutic interventions. Int. J. Mol. Sci. 24, 16255.
- Noman, M. Z., Parpal, S., Van Moer, K., Xiao, M., Yu, Y., Viklund, J., De Milito, A., Hasmim, M., Andersson, M., Amaravadi, R. K., Martinsson, J., Berchem, G. and Janji, B. (2020) Inhibition of Vps34 reprograms cold into hot inflamed tumors and improves anti-PD-1/ PD-L1 immunotherapy. Sci. Adv. 6, eaax7881.
- Obara, K. and Ohsumi, Y. (2011) Atg14: a key player in orchestrating autophagy. Int. J. Cell Biol. 2011, 713435.
- Obara, K., Sekito, T., Niimi, K. and Ohsumi, Y. (2008) The Atg18-Atg2 complex is recruited to autophagic membranes via phosphatidylinositol 3-phosphate and exerts an essential function. J. Biol. Chem. 283, 23972-23980.
- Ohashi, Y. (2021) Activation mechanisms of the VPS34 complexes. Cells 10, 3124.
- Ohashi, Y., Tremel, S., Masson, G. R., McGinney, L., Boulanger, J., Rostislavleva, K., Johnson, C. M., Niewczas, I., Clark, J. and Williams, R. L. (2020) Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes. Elife 9, e58281.
- Ohashi, Y., Tremel, S. and Williams, R. L. (2019) VPS34 complexes from a structural perspective. J. Lipid Res. 60, 229-241.
- Osawa, T. and Noda, N. N. (2019) Atg2: a novel phospholipid transfer protein that mediates de novo autophagosome biogenesis. Protein Sci. 28, 1005-1012.
- Parekh, V. V., Pabbisetty, S. K., Wu, L., Sebzda, E., Martinez, J., Zhang, J. and Van Kaer, L. (2017) Autophagy-related protein Vps34 controls the homeostasis and function of antigen cross-presenting CD8alpha(+) dendritic cells. Proc.Natl. Acad. Sci. U. S. A. 114, E6371-E6380.
- Parekh, V. V., Wu, L., Boyd, K. L., Williams, J. A., Gaddy, J. A., Olivares-Villagomez, D., Cover, T. L., Zong, W. X., Zhang, J. and Van Kaer, L. (2013) Impaired autophagy, defective T cell homeostasis, and a wasting syndrome in mice with a T cell-specific deletion of Vps34. J. Immunol. 190, 5086-5101.
- Park, J. M., Jung, C. H., Seo, M., Otto, N. M., Grunwald, D., Kim, K. H., Moriarity, B., Kim, Y. M., Starker, C., Nho, R. S., Voytas, D. and Kim, D. H. (2016) The ULK1 complex mediates MTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating ATG14. Autophagy 12, 547-564.
- Park, J. M., Lee, D. H. and Kim, D. H. (2023) Redefining the role of AMPK in autophagy and the energy stress response. Nat. Commun. 14, 2994.
- Park, J. M., Seo, M., Jung, C. H., Grunwald, D., Stone, M., Otto, N. M., Toso, E., Ahn, Y., Kyba, M., Griffin, T. J., Higgins, L. and Kim, D. H. (2018) ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction. Autophagy 14, 584-597.
- Pasquier, B. (2015) SAR405, a PIK3C3/Vps34 inhibitor that prevents autophagy and synergizes with MTOR inhibition in tumor cells. Autophagy 11, 725-726.
- Pavlinov, I., Salkovski, M. and Aldrich, L. N. (2020) Beclin 1-ATG14L protein-protein interaction inhibitor selectively inhibits autophagy through disruption of VPS34 Complex I. J. Am. Chem. Soc. 142, 8174-8182.
- Postoak, J. L., Song, W., Yang, G., Guo, X., Xiao, S., Saffold, C. E., Zhang, J., Joyce, S., Manley, N. R., Wu, L. and Van Kaer, L. (2022) Thymic epithelial cells require lipid kinase Vps34 for CD4 but not CD8 T cell selection. J. Exp. Med. 219, e20212554
- Qian, X., Li, X., Cai, Q., Zhang, C., Yu, Q., Jiang, Y., Lee, J. H., Hawke, D., Wang, Y., Xia, Y., Zheng, Y., Jiang, B. H., Liu, D. X., Jiang, T. and Lu, Z. (2017) Phosphoglycerate kinase 1 phosphorylates Beclin1 to induce autophagy. Mol. Cell 65, 917-931.e6.
- Rajala, A., He, F., Anderson, R. E., Wensel, T. G. and Rajala, R. V. S. (2020) Loss of class III phosphoinositide 3-kinase Vps34 results in cone degeneration. Biology (Basel) 9, 384.
- Reidick, C., Boutouja, F. and Platta, H. W. (2017) The class III phosphatidylinositol 3-kinase Vps34 in Saccharomyces cerevisiae. Biol. Chem. 398, 677-685.
- Robke, L., Laraia, L., Carnero Corrales, M. A., Konstantinidis, G., Muroi, M., Richters, A., Winzker, M., Engbring, T., Tomassi, S., Watanabe, N., Osada, H., Rauh, D., Waldmann, H., Wu, Y. W. and Engel, J. (2017) Phenotypic identification of a novel autophagy inhibitor chemotype targeting lipid kinase VPS34. Angew. Chem. Int. Ed. Engl. 56, 8153-8157.
- Ronan, B., Flamand, O., Vescovi, L., Dureuil, C., Durand, L., Fassy, F., Bachelot, M. F., Lamberton, A., Mathieu, M., Bertrand, T., Marquette, J. P., El-Ahmad, Y., Filoche-Romme, B., Schio, L., GarciaEcheverria, C., Goulaouic, H. and Pasquier, B. (2014) A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. Nat. Chem. Biol. 10, 1013-1019.
- Rostislavleva, K., Soler, N., Ohashi, Y., Zhang, L., Pardon, E., Burke, J. E., Masson, G. R., Johnson, C., Steyaert, J., Ktistakis, N. T. and Williams, R. L. (2015) Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science 350, aac7365.
- Russell, R. C., Tian, Y., Yuan, H., Park, H. W., Chang, Y. Y., Kim, J., Kim, H., Neufeld, T. P., Dillin, A. and Guan, K. L. (2013) ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat. Cell Biol. 15, 741-750.
- Schreiber, A., Collins, B. C., Davis, C., Enchev, R. I., Sedra, A., D'Antuono, R., Aebersold, R. and Peter, M. (2021) Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation. Mol. Cell 81, 5066-5081.
- Schu, P. V., Takegawa, K., Fry, M. J., Stack, J. H., Waterfield, M. D. and Emr, S. D. (1993) Phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for protein sorting. Science 260, 88-91.
- Scott, C. C., Vacca, F. and Gruenberg, J. (2014) Endosome maturation, transport and functions. Semin. Cell Dev. Biol. 31, 2-10.
- Simonsen, A., Lippe, R., Christoforidis, S., Gaullier, J. M., Brech, A., Callaghan, J., Toh, B. H., Murphy, C., Zerial, M. and Stenmark, H. (1998) EEA1 links PI(3)K function to Rab5 regulation of endosome fusion. Nature 394, 494-498.
- Simonsen, A. and Tooze, S. A. (2009) Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J. Cell Biol. 186, 773-782.
- Song, W., Postoak, J. L., Yang, G., Guo, X., Pua, H. H., Bader, J., Rathmell, J. C., Kobayashi, H., Haase, V. H., Leaptrot, K. L., Schrimpe-Rutledge, A. C., Sherrod, S. D., McLean, J. A., Zhang, J., Wu, L. and Van Kaer, L. (2023) Lipid kinase PIK3C3 maintains healthy brown and white adipose tissues to prevent metabolic diseases. Proc. Natl. Acad. Sci. U. S. A. 120, e2214874120.
- Stack, J. H., DeWald, D. B., Takegawa, K. and Emr, S. D. (1995) Vesicle-mediated protein transport: regulatory interactions between the Vps15 protein kinase and the Vps34 PtdIns 3-kinase essential for protein sorting to the vacuole in yeast. J. Cell Biol. 129, 321-334.
- Stack, J. H. and Emr, S. D. (1994) Vps34p required for yeast vacuolar protein sorting is a multiple specificity kinase that exhibits both protein kinase and phosphatidylinositol-specific PI 3-kinase activities. J. Biol. Chem. 269, 31552-31562.
- Stack, J. H., Herman, P. K., Schu, P. V. and Emr, S. D. (1993) A membrane-associated complex containing the Vps15 protein kinase and the Vps34 PI 3-kinase is essential for protein sorting to the yeast lysosome-like vacuole. EMBO J. 12, 2195-2204.
- Stempels, F. C., Janssens, M. H., Ter Beest, M., Mesman, R. J., Revelo, N. H., Ioannidis, M. and van den Bogaart, G. (2022) Novel and conventional inhibitors of canonical autophagy differently affect LC3-associated phagocytosis. FEBS Lett. 596, 491-509.
- Stjepanovic, G., Baskaran, S., Lin, M. G. and Hurley, J. H. (2017) Vps34 kinase domain dynamics regulate the autophagic PI 3-kinase complex. Mol. Cell 67, 528-534.e3.
- Sun, X., Du, J., Meng, H., Liu, F., Yang, N., Deng, S., Wan, H., Ye, D., Song, E. and Zeng, H. (2023) Targeting autophagy with SAR405 alleviates doxorubicin-induced cardiotoxicity. Cell Biol. Toxicol. 39, 3255-3267.
- Suzuki, K., Kubota, Y., Sekito, T. and Ohsumi, Y. (2007) Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells 12, 209-218.
- Suzuki, S. W., Yamamoto, H., Oikawa, Y., Kondo-Kakuta, C., Kimura, Y., Hirano, H. and Ohsumi, Y. (2015) Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation. Proc. Natl. Acad. Sci. U. S. A. 112, 3350-3355.
- Tamargo-Gomez, I. and Marino, G. (2018) AMPK: regulation of metabolic dynamics in the context of autophagy. Int. J. Mol. Sci. 19, 3812.
- Tao, H., Yancey, P. G., Blakemore, J. L., Zhang, Y., Ding, L., Jerome, W. G., Brown, J. D., Vickers, K. C. and Linton, M. F. (2021) Macrophage SR-BI modulates autophagy via VPS34 complex and PPA-Ralpha transcription of Tfeb in atherosclerosis. J. Clin. Invest. 131, e94229.
- Tremel, S., Ohashi, Y., Morado, D. R., Bertram, J., Perisic, O., Brandt, L. T. L., von Wrisberg, M. K., Chen, Z. A., Maslen, S. L., Kovtun, O., Skehel, M., Rappsilber, J., Lang, K., Munro, S., Briggs, J. A. G. and Williams, R. L. (2021) Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Nat. Commun. 12, 1564.
- Valet, C., Levade, M., Chicanne, G., Bilanges, B., Cabou, C., Viaud, J., Gratacap, M. P., Gaits-Iacovoni, F., Vanhaesebroeck, B., Payrastre, B. and Severin, S. (2017) A dual role for the class III PI3K, Vps34, in platelet production and thrombus growth. Blood 130, 2032-2042.
- Vanhaesebroeck, B., Guillermet-Guibert, J., Graupera, M. and Bilanges, B. (2010) The emerging mechanisms of isoform-specific PI3K signalling. Nat. Rev. Mol. Cell Biol. 11, 329-341.
- Wang, K., Kong, F., Qiu, Y., Chen, T., Fu, J., Jin, X., Su, Y., Gu, Y., Hu, Z. and Li, J. (2023) Autophagy regulation and protein kinase activity of PIK3C3 controls sertoli cell polarity through its negative regulation on SCIN (scinderin). Autophagy 19, 2934-2957.
- Williams, C. G., Jureka, A. S., Silvas, J. A., Nicolini, A. M., Chvatal, S. A., Carlson-Stevermer, J., Oki, J., Holden, K. and Basler, C. F. (2021) Inhibitors of VPS34 and fatty-acid metabolism suppress SARS-CoV-2 replication. Cell Rep. 36, 109479.
- Wold, M. S., Lim, J., Lachance, V., Deng, Z. and Yue, Z. (2016) ULK1-mediated phosphorylation of ATG14 promotes autophagy and is impaired in Huntington's disease models. Mol. Neurodegener. 11, 76.
- Wong, P. M., Puente, C., Ganley, I. G. and Jiang, X. (2013) The ULK1 complex: sensing nutrient signals for autophagy activation. Autophagy 9, 124-137.
- Wu, Q., Zhou, D., Shen, Z., Chen, B., Wang, G., Wu, L., Zhang, L., Li, X., Yuan, L., Wu, Y., Qu, N. and Zhou, W. (2023) VPS34-IN1 induces apoptosis of ER+ breast cancer cells via activating PERK/ATF4/CHOP pathway. Biochem. Pharmacol. 214, 115634.
- Wu, S., He, Y., Qiu, X., Yang, W., Liu, W., Li, X., Li, Y., Shen, H. M., Wang, R., Yue, Z. and Zhao, Y. (2018) Targeting the potent Beclin 1-UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking. Proc. Natl. Acad. Sci. U. S. A. 115, E5669-E5678.
- Xiong, X., Tao, R., DePinho, R. A. and Dong, X. C. (2012) The autophagy-related gene 14 (Atg14) is regulated by forkhead box O transcription factors and circadian rhythms and plays a critical role in hepatic autophagy and lipid metabolism. J. Biol. Chem. 287, 39107-39114.
- Yan, Y., Flinn, R. J., Wu, H., Schnur, R. S. and Backer, J. M. (2009) hVps15, but not Ca2+/CaM, is required for the activity and regulation of hVps34 in mammalian cells. Biochem. J. 417, 747-755.
- Ye, J., Zhang, J., Zhu, Y., Wang, L., Jiang, X., Liu, B. and He, G. (2023) Targeting autophagy and beyond: deconvoluting the complexity of Beclin-1 from biological function to cancer therapy. Acta Pharm. Sin. B 13, 4688-4714.
- Young, L. N., Goerdeler, F. and Hurley, J. H. (2019) Structural pathway for allosteric activation of the autophagic PI 3-kinase complex I. Proc. Natl. Acad. Sci. U. S. A. 116, 21508-21513.
- Yuan, H. X., Russell, R. C. and Guan, K. L. (2013) Regulation of PIK3C3/VPS34 complexes by MTOR in nutrient stress-induced autophagy. Autophagy 9, 1983-1995.
- Zhang, D., Wang, W., Sun, X., Xu, D., Wang, C., Zhang, Q., Wang, H., Luo, W., Chen, Y., Chen, H. and Liu, Z. (2016) AMPK regulates autophagy by phosphorylating BECN1 at threonine 388. Autophagy 12, 1447-1459.