1. Vézina, C., Kudelski, A., and Sehgal, S.N. (1975). Rapamycin (AY-22,989), a new
antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of
the active principle. J. Antibiot. (Tokyo) 28, 721–726. 10.7164/antibiotics.28.721.
2. Douros, J., and Suffness, M. (1981). New antitumor substances of natural origin.
Cancer Treat. Rev. 8, 63–87. 10.1016/S0305-7372(81)80006-0.
3. Martel, R.R., Klicius, J., and Galet, S. (1977). Inhibition of the immune response by
rapamycin, a new antifungal antibiotic. Can. J. Physiol. Pharmacol. 55, 48–51.
10.1139/y77-007.
4. Rosen, M., Standaert, R., Galat, A., Nakatsuka, M., and Schreiber, S. (1990).
Inhibition of FKBP Rotamase Activity by Immunosuppressant FK506: Twisted
Amide Surrogate. Science 248, 863–866. 10.1126/science.1693013.
5. Standaert, R.F., Galat, A., Verdine, G.L., and Schreiber, S.L. (1990). Molecular
cloning and overexpression of the human FKS06-binding protein FKBP. Nature 346,
671–674. 10.1038/346671a0.
6. Heitman, J., Movva, N.R., and Hall, M.N. (1991). Targets for cell cycle arrest by the
immunosuppressant rapamycin in yeast. Science 253, 905–909.
10.1126/science.1715094.
7. Chen, J., Zheng, X.F., Brown, E.J., and Schreiber, S.L. (1995). Identification of an
11-kDa FKBP12-rapamycin-binding domain within the 289-kDa FKBP12-
70
rapamycin-associated protein and characterization of a critical serine residue. Proc.
Natl. Acad. Sci. 92, 4947–4951. 10.1073/pnas.92.11.4947.
8. Sabatini, D.M., Erdjument-Bromage, H., Lui, M., Tempst, P., and Snyder, S.H.
(1994). RAFT1: A mammalian protein that binds to FKBP12 in a rapamycindependent fashion and is homologous to yeast TORs. Cell 78, 35–43. 10.1016/00928674(94)90570-3.
9. Sabers, C.J., Martin, M.M., Brunn, G.J., Williams, J.M., Dumont, F.J., Wiederrecht,
G., and Abraham, R.T. (1995). Isolation of a Protein Target of the FKBP12Rapamycin Complex in Mammalian Cells (∗). J. Biol. Chem. 270, 815–822.
10.1074/jbc.270.2.815.
10. Noda, T., and Ohsumi, Y. (1998). Tor, a phosphatidylinositol kinase homologue,
controls autophagy in yeast. J. Biol. Chem. 273, 3963–3966. 10.1074/jbc.273.7.3963.
11. Jacinto, E., Loewith, R., Schmidt, A., Lin, S., Rüegg, M.A., Hall, A., and Hall,
M.N. (2004). Mammalian TOR complex 2 controls the actin cytoskeleton and is
rapamycin insensitive. Nat. Cell Biol. 6, 1122–1128. 10.1038/ncb1183.
12. Loewith, R., Jacinto, E., Wullschleger, S., Lorberg, A., Crespo, J.L., Bonenfant, D.,
Oppliger, W., Jenoe, P., and Hall, M.N. (2002). Two TOR Complexes, Only One of
which Is Rapamycin Sensitive, Have Distinct Roles in Cell Growth Control. Mol.
Cell 10, 457–468. 10.1016/S1097-2765(02)00636-6.
13. Sarbassov, Ali, S.M., Kim, D.-H., Guertin, D.A., Latek, R.R., Erdjument-Bromage,
H., Tempst, P., and Sabatini, D.M. (2004). Rictor, a Novel Binding Partner of
71
mTOR, Defines a Rapamycin-Insensitive and Raptor-Independent Pathway that
Regulates the Cytoskeleton. Curr. Biol. 14, 1296–1302. 10.1016/j.cub.2004.06.054.
14. Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C.,
Avruch, J., and Yonezawa, K. (2002). Raptor, a Binding Partner of Target of
Rapamycin (TOR), Mediates TOR Action. Cell 110, 177–189. 10.1016/S00928674(02)00833-4.
15. Kim, D.-H., Sarbassov, D.D., Ali, S.M., Latek, R.R., Guntur, K.V.P., ErdjumentBromage, H., Tempst, P., and Sabatini, D.M. (2003). GβL, a Positive Regulator of
the Rapamycin-Sensitive Pathway Required for the Nutrient-Sensitive Interaction
between Raptor and mTOR. Mol. Cell 11, 895–904. 10.1016/S1097-2765(03)00114X.
16. Kim, D.-H., Sarbassov, D.D., Ali, S.M., King, J.E., Latek, R.R., ErdjumentBromage, H., Tempst, P., and Sabatini, D.M. (2002). mTOR Interacts with Raptor to
Form a Nutrient-Sensitive Complex that Signals to the Cell Growth Machinery. Cell
110, 163–175. 10.1016/S0092-8674(02)00808-5.
17. Peterson, T.R., Laplante, M., Thoreen, C.C., Sancak, Y., Kang, S.A., Kuehl, W.M.,
Gray, N.S., and Sabatini, D.M. (2009). DEPTOR Is an mTOR Inhibitor Frequently
Overexpressed in Multiple Myeloma Cells and Required for Their Survival. Cell 137,
873–886. 10.1016/j.cell.2009.03.046.
18. Wang, L., Harris, T.E., Roth, R.A., and Lawrence, J.C. (2007). PRAS40 Regulates
mTORC1 Kinase Activity by Functioning as a Direct Inhibitor of Substrate Binding.
72
J. Biol. Chem. 282, 20036–20044. 10.1074/jbc.M702376200.
19. Frias, M.A., Thoreen, C.C., Jaffe, J.D., Schroder, W., Sculley, T., Carr, S.A., and
Sabatini, D.M. (2006). mSin1 Is Necessary for Akt/PKB Phosphorylation, and Its
Isoforms Define Three Distinct mTORC2s. Curr. Biol. 16, 1865–1870.
10.1016/j.cub.2006.08.001.
20. Jacinto, E., Facchinetti, V., Liu, D., Soto, N., Wei, S., Jung, S.Y., Huang, Q., Qin,
J., and Su, B. (2006). SIN1/MIP1 Maintains rictor-mTOR Complex Integrity and
Regulates Akt Phosphorylation and Substrate Specificity. Cell 127, 125–137.
10.1016/j.cell.2006.08.033.
21. Woo, S.-Y., Kim, D.-H., Jun, C.-B., Kim, Y.-M., Haar, E.V., Lee, S., Hegg, J.W.,
Bandhakavi, S., Griffin, T.J., and Kim, D.-H. (2007). PRR5, a Novel Component of
mTOR Complex 2, Regulates Platelet-derived Growth Factor Receptor β Expression
and Signaling. J. Biol. Chem. 282, 25604–25612. 10.1074/jbc.M704343200.
22. Yang, Q., Inoki, K., Ikenoue, T., and Guan, K.-L. (2006). Identification of Sin1 as
an essential TORC2 component required for complex formation and kinase activity.
Genes Dev. 20, 2820–2832. 10.1101/gad.1461206.
23. Reinke, A., Anderson, S., McCaffery, J.M., Yates, J., Aronova, S., Chu, S.,
Fairclough, S., Iverson, C., Wedaman, K.P., and Powers, T. (2004). TOR Complex 1
Includes a Novel Component, Tco89p (YPL180w), and Cooperates with Ssd1p to
Maintain Cellular Integrity in Saccharomyces cerevisiae. J. Biol. Chem. 279, 14752–
14762. 10.1074/jbc.M313062200.
73
24. Wedaman, K.P., Reinke, A., Anderson, S., Yates, J., McCaffery, J.M., and Powers,
T. (2003). Tor Kinases Are in Distinct Membrane-associated Protein Complexes in
Saccharomyces cerevisiae. Mol. Biol. Cell 14, 1204–1220. 10.1091/mbc.e02-090609.
25. Zinzalla, V., Sturgill, T.W., and Hall, M.N. (2010). Chapter 1 - TOR Complexes:
Composition, Structure, and Phosphorylation. In The Enzymes The Enzymes.
(Academic Press), pp. 1–20. 10.1016/S1874-6047(10)27001-4.
26. Loewith, R., and Hall, M.N. (2011). Target of rapamycin (TOR) in nutrient
signaling and growth control. Genetics 189, 1177–1201.
10.1534/genetics.111.133363.
27. Urban, J., Soulard, A., Huber, A., Lippman, S., Mukhopadhyay, D., Deloche, O.,
Wanke, V., Anrather, D., Ammerer, G., Riezman, H., et al. (2007). Sch9 is a major
target of TORC1 in Saccharomyces cerevisiae. Mol. Cell 26, 663–674.
10.1016/j.molcel.2007.04.020.
28. Noda, T. (2017). Regulation of Autophagy through TORC1 and mTORC1.
Biomolecules 7, 52. 10.3390/biom7030052.
29. Lempiäinen, H., Uotila, A., Urban, J., Dohnal, I., Ammerer, G., Loewith, R., and
Shore, D. (2009). Sfp1 interaction with TORC1 and Mrs6 reveals feedback
regulation on TOR signaling. Mol. Cell 33, 704–716. 10.1016/j.molcel.2009.01.034.
30. Bertram, P.G., Choi, J.H., Carvalho, J., Ai, W., Zeng, C., Chan, T.-F., and Zheng,
X.F.S. (2000). Tripartite Regulation of Gln3p by TOR, Ure2p, and Phosphatases. J.
74
Biol. Chem. 275, 35727–35733. 10.1074/jbc.M004235200.
31. Boeckstaens, M., Llinares, E., Van Vooren, P., and Marini, A.M. (2014). The
TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium
transport protein. Nat. Commun. 5, 3101. 10.1038/ncomms4101.
32. Yerlikaya, S., Meusburger, M., Kumari, R., Huber, A., Anrather, D., Costanzo, M.,
Boone, C., Ammerer, G., Baranov, P.V., and Loewith, R. (2016). TORC1 and
TORC2 work together to regulate ribosomal protein S6 phosphorylation in
Saccharomyces cerevisiae. Mol. Biol. Cell 27, 397–409. 10.1091/mbc.e15-08-0594.
33. Inoki, K., Li, Y., Xu, T., and Guan, K.-L. (2003). Rheb GTPase is a direct target of
TSC2 GAP activity and regulates mTOR signaling. Genes Dev. 17, 1829–1834.
10.1101/gad.1110003.
34. Inoki, K., Li, Y., Zhu, T., Wu, J., and Guan, K.-L. (2002). TSC2 is phosphorylated
and inhibited by Akt and suppresses mTOR signalling. Nat. Cell Biol. 4, 648–657.
10.1038/ncb839.
35. Potter, C.J., Huang, H., and Xu, T. (2001). Drosophila Tsc1 Functions with Tsc2 to
Antagonize Insulin Signaling in Regulating Cell Growth, Cell Proliferation, and
Organ Size. Cell 105, 357–368. 10.1016/S0092-8674(01)00333-6.
36. Hao, F., Kondo, K., Itoh, T., Ikari, S., Nada, S., Okada, M., and Noda, T. (2017).
Rheb localized on the Golgi membrane activates lysosome-localized mTORC1 at the
Golgi-lysosome contact site. J. Cell Sci., jcs.208017. 10.1242/jcs.208017.
37. Bar-Peled, L., Schweitzer, L.D., Zoncu, R., and Sabatini, D.M. (2012). Ragulator Is
75
a GEF for the Rag GTPases that Signal Amino Acid Levels to mTORC1. Cell 150,
1196–1208. 10.1016/j.cell.2012.07.032.
38. Sancak, Y., Bar-Peled, L., Zoncu, R., Markhard, A.L., Nada, S., and Sabatini, D.M.
(2010). Ragulator-Rag complex targets mTORC1 to the lysosomal surface and Is
necessary for Its activation by amino acids. Cell 141, 290–303.
10.1016/j.cell.2010.02.024.
39. Kim, E., Goraksha-Hicks, P., Li, L., Neufeld, T.P., and Guan, K.-L. (2008).
Regulation of TORC1 by Rag GTPases in nutrient response. Nat. Cell Biol. 10, 935–
945. 10.1038/ncb1753.
40. Sancak, Y., Peterson, T.R., Shaul, Y.D., Lindquist, R.A., Thoreen, C.C., Bar-Peled,
L., and Sabatini, D.M. (2008). The Rag GTPases bind raptor and mediate amino acid
signaling to mTORC1. Science 320, 1496–1501. 10.1126/science.1157535.
41. Jewell, J.L., Russell, R.C., and Guan, K.-L. (2013). Amino acid signalling upstream
of mTOR. Nat. Rev. Mol. Cell Biol. 14, 133–139. 10.1038/nrm3522.
42. Binda, M., Péli-Gulli, M.-P., Bonfils, G., Panchaud, N., Urban, J., Sturgill, T.W.,
Loewith, R., and De Virgilio, C. (2009). The Vam6 GEF controls TORC1 by
activating the EGO Complex. Mol. Cell 35, 563–573. 10.1016/j.molcel.2009.06.033.
43. Powis, K., Zhang, T., Panchaud, N., Wang, R., Virgilio, C.D., and Ding, J. (2015).
Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag
GTPase-dependent TORC1 signaling. Cell Res. 25, 1043–1059. 10.1038/cr.2015.86.
44. Bar-Peled, L., Chantranupong, L., Cherniack, A.D., Chen, W.W., Ottina, K.A.,
76
Grabiner, B.C., Spear, E.D., Carter, S.L., Meyerson, M., and Sabatini, D.M. (2013).
A Tumor suppressor complex with GAP activity for the Rag GTPases That signal
amino acid sufficiency to mTORC1. Science 340, 1100–1106.
10.1126/science.1232044.
45. Condon, K.J., and Sabatini, D.M. (2019). Nutrient regulation of mTORC1 at a
glance. J. Cell Sci. 132, jcs222570. 10.1242/jcs.222570.
46. Algret, R., Fernandez-Martinez, J., Shi, Y., Kim, S.J., Pellarin, R., Cimermancic,
P., Cochet, E., Sali, A., Chait, B.T., Rout, M.P., et al. (2014). Molecular Architecture
and Function of the SEA Complex, a Modulator of the TORC1 Pathway. Mol. Cell.
Proteomics MCP 13, 2855–2870. 10.1074/mcp.M114.039388.
47. Kira, S., Tabata, K., Shirahama-Noda, K., Nozoe, A., Yoshimori, T., and Noda, T.
(2014). Reciprocal conversion of Gtr1 and Gtr2 nucleotide-binding states by Npr2Npr3 inactivates TORC1 and induces autophagy. Autophagy 10, 1565–1578.
10.4161/auto.29397.
48. Panchaud, N., Péli-Gulli, M.-P., and De Virgilio, C. (2013). SEACing the GAP that
nEGOCiates TORC1 activation: Evolutionary conservation of Rag GTPase
regulation. Cell Cycle 12, 2948–2952. 10.4161/cc.26000.
49. Panchaud, N., Péli-Gulli, M.-P., and De Virgilio, C. (2013). Amino acid
deprivation inhibits TORC1 through a GTPase-activating protein complex for the
Rag family GTPase Gtr1. Sci. Signal. 6. 10.1126/scisignal.2004112.
50. Nicastro, R., Sardu, A., Panchaud, N., and De Virgilio, C. (2017). The Architecture
77
of the Rag GTPase Signaling Network. Biomolecules 7, 48. 10.3390/biom7030048.
51. Kim, A., and Cunningham, K.W. (2015). A LAPF/phafin1-like protein regulates
TORC1 and lysosomal membrane permeabilization in response to endoplasmic
reticulum membrane stress. Mol. Biol. Cell 26, 4631–4645. 10.1091/mbc.E15-080581.
52. Michel, A.H., Hatakeyama, R., Kimmig, P., Arter, M., Peter, M., Matos, J., De
Virgilio, C., and Kornmann, B. (2017). Functional mapping of yeast genomes by
saturated transposition. eLife 6, e23570. 10.7554/eLife.23570.
53. Tanigawa, M., and Maeda, T. (2017). An In Vitro TORC1 Kinase Assay That
Recapitulates the Gtr-Independent Glutamine-Responsive TORC1 Activation
Mechanism on Yeast Vacuoles. Mol. Cell. Biol. 37, e00075-17.
10.1128/MCB.00075-17.
54. Ukai, H., Araki, Y., Kira, S., Oikawa, Y., May, A.I., and Noda, T. (2018). Gtr/Egoindependent TORC1 activation is achieved through a glutamine-sensitive interaction
with Pib2 on the vacuolar membrane. PLOS Genet. 14, e1007334.
10.1371/journal.pgen.1007334.
55. Chantranupong, L., Wolfson, R.L., Orozco, J.M., Saxton, R.A., Scaria, S.M., BarPeled, L., Spooner, E., Isasa, M., Gygi, S.P., and Sabatini, D.M. (2014). The Sestrins
Interact with GATOR2 to Negatively Regulate the Amino-Acid-Sensing Pathway
Upstream of mTORC1. Cell Rep. 9, 1–8. 10.1016/j.celrep.2014.09.014.
56. Parmigiani, A., Nourbakhsh, A., Ding, B., Wang, W., Kim, Y.C., Akopiants, K.,
78
Guan, K.-L., Karin, M., and Budanov, A.V. (2014). Sestrins Inhibit mTORC1 Kinase
Activation through the GATOR Complex. Cell Rep. 9, 1281–1291.
10.1016/j.celrep.2014.10.019.
57. Saxton, R.A., Knockenhauer, K.E., Wolfson, R.L., Chantranupong, L., Pacold,
M.E., Wang, T., Schwartz, T.U., and Sabatini, D.M. (2016). Structural basis for
leucine sensing by the Sestrin2-mTORC1 pathway. Science 351, 53–58.
10.1126/science.aad2087.
58. Wolfson, R.L., Chantranupong, L., Saxton, R.A., Shen, K., Scaria, S.M., Cantor,
J.R., and Sabatini, D.M. (2016). Sestrin2 is a leucine sensor for the mTORC1
pathway. Science 351, 43–48. 10.1126/science.aab2674.
59. Chantranupong, L., Scaria, S.M., Saxton, R.A., Gygi, M.P., Shen, K., Wyant, G.A.,
Wang, T., Harper, J.W., Gygi, S.P., and Sabatini, D.M. (2016). The CASTOR
Proteins Are Arginine Sensors for the mTORC1 Pathway. Cell 165, 153–164.
10.1016/j.cell.2016.02.035.
60. Saxton, R.A., Chantranupong, L., Knockenhauer, K.E., Schwartz, T.U., and
Sabatini, D.M. (2016). Mechanism of arginine sensing by CASTOR1 upstream of
mTORC1. Nature 536, 229–233. 10.1038/nature19079.
61. Gu, X., Orozco, J.M., Saxton, R.A., Condon, K.J., Liu, G.Y., Krawczyk, P.A.,
Scaria, S.M., Harper, J.W., Gygi, S.P., and Sabatini, D.M. (2017). SAMTOR is an S adenosylmethionine sensor for the mTORC1 pathway. Science 358, 813–818.
10.1126/science.aao3265.
79
62. Chen, J., Ou, Y., Luo, R., Wang, J., Wang, D., Guan, J., Li, Y., Xia, P., Chen, P.R.,
and Liu, Y. (2021). SAR1B senses leucine levels to regulate mTORC1 signalling.
Nature 596, 281–284. 10.1038/s41586-021-03768-w.
63. Bonfils, G., Jaquenoud, M., Bontron, S., Ostrowicz, C., Ungermann, C., and
De Virgilio, C. (2012). Leucyl-tRNA Synthetase Controls TORC1 via the EGO
Complex. Mol. Cell 46, 105–110. 10.1016/j.molcel.2012.02.009.
64. Sutter, B.M., Wu, X., Laxman, S., and Tu, B.P. (2013). Methionine Inhibits
Autophagy and Promotes Growth by Inducing the SAM-Responsive Methylation of
PP2A. Cell 154, 403–415. 10.1016/j.cell.2013.06.041.
65. Tanigawa, M., Yamamoto, K., Nagatoishi, S., Nagata, K., Noshiro, D., Noda, N.N.,
Tsumoto, K., and Maeda, T. (2021). A glutamine sensor that directly activates
TORC1. Commun. Biol. 4, 1093. 10.1038/s42003-021-02625-w.
66. Chantranupong, L., Wolfson, R.L., and Sabatini, D.M. (2015). Nutrient-sensing
mechanisms across evolution. Cell 161, 67–83. 10.1016/j.cell.2015.02.041.
67. Jin, N., Mao, K., Jin, Y., Tevzadze, G., Kauffman, E.J., Park, S., Bridges, D.,
Loewith, R., Saltiel, A.R., Klionsky, D.J., et al. (2014). Roles for PI(3,5)P 2 in
nutrient sensing through TORC1. Mol. Biol. Cell 25, 1171–1185. 10.1091/mbc.e1401-0021.
68. Kamada, Y., Yoshino, K., Kondo, C., Kawamata, T., Oshiro, N., Yonezawa, K.,
and Ohsumi, Y. (2010). Tor directly controls the Atg1 Kinase complex to regulate
autophagy. Mol. Cell. Biol. 30, 1049–1058. 10.1128/MCB.01344-09.
80
69. Suzuki, H., Osawa, T., Fujioka, Y., and Noda, N.N. (2017). Structural biology of
the core autophagy machinery. Curr. Opin. Struct. Biol. 43, 10–17.
10.1016/j.sbi.2016.09.010.
70. Suzuki, K., and Ohsumi, Y. (2010). Current knowledge of the pre-autophagosomal
structure (PAS). FEBS Lett 584, 1280–1286. 10.1016/j.febslet.2010.02.001.
71. Fujioka, Y., Alam, J.Md., Noshiro, D., Mouri, K., Ando, T., Okada, Y., May, A.I.,
Knorr, R.L., Suzuki, K., Ohsumi, Y., et al. (2020). Phase separation organizes the site
of autophagosome formation. Nature 578, 301–305. 10.1038/s41586-020-1977-6.
72. Kira, S., Kumano, Y., Ukai, H., Takeda, E., Matsuura, A., and Noda, T. (2016).
Dynamic relocation of the TORC1–Gtr1/2–Ego1/2/3 complex is regulated by Gtr1
and Gtr2. Mol. Biol. Cell 27, 382–396. 10.1091/mbc.e15-07-0470.
73. Wolfson, R.L., Chantranupong, L., Saxton, R.A., Shen, K., Scaria, S.M., Cantor,
J.R., and Sabatini, D.M. (2016). Sestrin2 is a leucine sensor for the mTORC1
pathway. Science 351, 43–48. 10.1126/science.aab2674.
74. Kim, A., and Cunningham, K.W. (2015). A LAPF/phafin1-like protein regulates
TORC1 and lysosomal membrane permeabilization in response to endoplasmic
reticulum membrane stress. Mol. Biol. Cell 26, 4631–4645. 10.1091/mbc.E15-080581.
75. Hatakeyama, R. (2021). Pib2 as an Emerging Master Regulator of Yeast TORC1.
Biomolecules 11, 1489. 10.3390/biom11101489.
76. Mudholkar, K., Fitzke, E., Prinz, C., Mayer, M.P., and Rospert, S. (2017). The
81
Hsp70 homolog Ssb affects ribosome biogenesis via the TORC1-Sch9 signaling
pathway. Nat. Commun. 8, 937. 10.1038/s41467-017-00635-z.
77. Mülleder, M., Capuano, F., Pir, P., Christen, S., Sauer, U., Oliver, S.G., and Ralser,
M. (2012). A prototrophic deletion mutant collection for yeast metabolomics and
systems biology. Nat. Biotechnol. 30, 1176–1178. 10.1038/nbt.2442.
78. Kira, S., Noguchi, M., Araki, Y., Oikawa, Y., Yoshimori, T., Miyahara, A., and
Noda, T. (2021). Vacuolar protein Tag1 and Atg1–Atg13 regulate autophagy
termination during persistent starvation in S. cerevisiae. J. Cell Sci. 134, jcs253682.
10.1242/jcs.253682.
79. Kotani, T., Kirisako, H., Koizumi, M., Ohsumi, Y., and Nakatogawa, H. (2018).
The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the
endoplasmic reticulum for autophagosome formation. Proc. Natl. Acad. Sci. 115,
10363–10368. 10.1073/pnas.1806727115.
80. Merhi, A., and André, B. (2012). Internal amino acids promote Gap1 permease
ubiquitylation via TORC1/Npr1/14-3-3-dependent control of the Bul arrestin-like
adaptors. Mol. Cell. Biol. 32, 4510–4522. 10.1128/MCB.00463-12.
81. Bianchi, F., Van’T Klooster, J.S., Ruiz, S.J., and Poolman, B. (2019). Regulation of
Amino Acid Transport in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 83,
e00024-19. 10.1128/MMBR.00024-19.
82. Kaur, J., and Bachhawat, A.K. (2007). Yct1p, a novel, high-affinity, cysteinespecific transporter from the yeast Saccharomyces cerevisiae. Genetics 176, 877–
82
890. 10.1534/genetics.107.070342.
83. Düring-Olsen, L., Regenberg, B., Gjermansen, C., Kielland-Brandt, M.C., and
Hansen, J. (1999). Cysteine uptake by Saccharomyces cerevisiae is accomplished by
multiple permeases. Curr. Genet. 35, 609–617. 10.1007/s002940050459.
84. Wu AL, M.-R.W. (1994). GSH1, which encodes gamma-glutamylcysteine
synthetase, is a target gene for yAP-1 transcriptional regulation. Mol. Cell. Biol. 14,
5832–5839. 10.1128/mcb.14.9.5832-5839.1994.
85. Kitamoto, K., Yoshizawa, K., Ohsumi, Y., and Anraku, Y. (1988). Dynamic
aspects of vacuolar and cytosolic amino acid pools of Saccharomyces cerevisiae. J.
Bacteriol. 170, 2683–2686. 10.1128/jb.170.6.2683-2686.1988.
86. Kitajima, T., Jigami, Y., and Chiba, Y. (2012). Cytotoxic Mechanism of
Selenomethionine in Yeast. J. Biol. Chem. 287, 10032–10038.
10.1074/jbc.M111.324244.
87. Paul, B.D., Sbodio, J.I., and Snyder, S.H. (2018). Cysteine Metabolism in Neuronal
Redox Homeostasis. Trends Pharmacol. Sci. 39, 513–524.
10.1016/j.tips.2018.02.007.
88. Yin, J., Ren, W., Yang, G., Duan, J., Huang, X., Fang, R., Li, C., Li, T., Yin, Y.,
Hou, Y., et al. (2016). L-Cysteine metabolism and its nutritional implications. Mol.
Nutr. Food Res. 60, 134–146. 10.1002/mnfr.201500031.
89. Thomas, D., and Surdin-Kerjan, Y. (1997). Metabolism of sulfur amino acids in
Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 61, 503–532.
83
10.1128/mmbr.61.4.503-532.1997.
90. Varlakhanova, N.V., Mihalevic, M., Bernstein, K.A., and Ford, M.G.J. (2017). Pib2
and EGO Complex are both required for activation of TORC1. J. Cell Sci.,
jcs.207910. 10.1242/jcs.207910.
91. Kawano-Kawada, M., Kakinuma, Y., and Sekito, T. (2018). Transport of Amino
Acids across the Vacuolar Membrane of Yeast: Its Mechanism and Physiological
Role. Biol. Pharm. Bull. 41, 1496–1501. 10.1248/bpb.b18-00165.
92. Stracka, D., Jozefczuk, S., Rudroff, F., Sauer, U., and Hall, M.N. (2014). Nitrogen
source activates TOR (target of rapamycin) complex 1 via glutamine and
independently of Gtr/Rag proteins. J. Biol. Chem. 289, 25010–25020.
10.1074/jbc.M114.574335.
93. Dokládal, L., Stumpe, M., Hu, Z., Jaquenoud, M., Dengjel, J., and De Virgilio, C.
(2021). Phosphoproteomic responses of TORC1 target kinases reveal discrete and
convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep.
37, 110149. 10.1016/j.celrep.2021.110149.
94. Albers, E., Laizé, V., Blomberg, A., Hohmann, S., and Gustafsson, L. (2003).
Ser3p (Yer081wp) and Ser33p (Yil074cp) Are Phosphoglycerate Dehydrogenases in
Saccharomyces cerevisiae. J. Biol. Chem. 278, 10264–10272.
10.1074/jbc.M211692200.
95. Napolitano, G., Di Malta, C., Esposito, A., De Araujo, M.E.G., Pece, S., Bertalot,
G., Matarese, M., Benedetti, V., Zampelli, A., Stasyk, T., et al. (2020). A substrate-
84
specific mTORC1 pathway underlies Birt–Hogg–Dubé syndrome. Nature 585, 597–
602. 10.1038/s41586-020-2444-0.
96. Morozumi, Y., Hishinuma, A., Furusawa, S., Sofyantoro, F., Tatebe, H., and
Shiozaki, K. (2021). Fission yeast TOR complex 1 phosphorylates Psk1 through an
evolutionarily conserved interaction mediated by the TOS motif. J. Cell Sci. 134,
jcs258865. 10.1242/jcs.258865.
97. Fan, S.-J., Snell, C., Turley, H., Li, J.-L., McCormick, R., Perera, S.M.W.,
Heublein, S., Kazi, S., Azad, A., Wilson, C., et al. (2016). PAT4 levels control
amino-acid sensitivity of rapamycin-resistant mTORC1 from the Golgi and affect
clinical outcome in colorectal cancer. Oncogene 35, 3004–3015.
10.1038/onc.2015.363.
98. Hatakeyama, R., Péli-Gulli, M.-P., Hu, Z., Jaquenoud, M., Garcia Osuna, G.M.,
Sardu, A., Dengjel, J., and De Virgilio, C. (2019). Spatially Distinct Pools of TORC1
Balance Protein Homeostasis. Mol. Cell 73, 325-338.e8.
10.1016/j.molcel.2018.10.040.
99. Meng, D., Yang, Q., Wang, H., Melick, C.H., Navlani, R., Frank, A.R., and Jewell,
J.L. (2020). Glutamine and asparagine activate mTORC1 independently of Rag
GTPases. J. Biol. Chem. 295, 2890–2899. 10.1074/jbc.AC119.011578.
100.
Baker Brachmann, C., Davies, A., Cost, G.J., Caputo, E., Li, J., Hieter, P., and
Boeke, J.D. (1998). Designer deletion strains derived fromSaccharomyces cerevisiae
S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and
85
other applications. Yeast 14, 115–132. 10.1002/(SICI)10970061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2.
101.
Sikorski, R.S., and Hieter, P. (1989). A System of Shuttle Vectors and Yeast
Host Strains Designed for Efficient Manipulation of DNA in Saccharomyces
ceratisiae. Genetics 122, 19–27. 10.1093/genetics/122.1.19.
102.
Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M., and Barton, G.J.
(2009). Jalview Version 2—a multiple sequence alignment editor and analysis
workbench. Bioinformatics 25, 1189–1191. 10.1093/bioinformatics/btp033.
103.
Janke, C., Magiera, M.M., Rathfelder, N., Taxis, C., Reber, S., Maekawa, H.,
Moreno-Borchart, A., Doenges, G., Schwob, E., Schiebel, E., et al. (2004). A
versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins,
more markers and promoter substitution cassettes. Yeast 21, 947–962.
10.1002/yea.1142.
104.
Storici, F., and Resnick, M.A. (2006). The Delitto Perfetto Approach to In
Vivo Site‐Directed Mutagenesis and Chromosome Rearrangements with Synthetic
Oligonucleotides in Yeast. In Methods in Enzymology (Elsevier), pp. 329–345.
10.1016/S0076-6879(05)09019-1.
105.
Cools, M., Rompf, M., Mayer, A., and André, B. (2019). Measuring the
Activity of Plasma Membrane and Vacuolar Transporters in Yeast. In Yeast Systems
Biology Methods in Molecular Biology., S. G. Oliver and J. I. Castrillo, eds.
(Springer New York), pp. 247–261. 10.1007/978-1-4939-9736-7_15.
86
106.
Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., and
Mann, M. (2005). Exponentially Modified Protein Abundance Index (emPAI) for
Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced
Peptides per Protein. Mol. Cell. Proteomics 4, 1265–1272. 10.1074/mcp.M500061MCP200.
87
Acknowledgements
First, I would like to express my deepest gratitude to my supervisor, Prof.
Takeshi Noda, for his continuous support, insightful guidance, and constructive
feedback, throughout my research journey. I would like to express my deep gratitude to
assistant professor Dr. Araki for his invaluable guidance and insightful discussion in
this study. I am thankful to all members of Noda-Lab for valuable discussion.
I would like to thank for Prof. Takayuki Sekito and Prof. Nobuo Noda for their
scientific discussions.
My heartfelt thanks go to my parents, for their unwavering love, support, and
encouragement throughout my academic journey. I am immensely grateful to my
spouse for her endless support, patience, and belief, and for always standing by my side,
providing unwavering support in both the good times and the challenging moments.
Finally, I want to express my gratitude to everyone who took the time to read
this thesis and provide me with valuable suggestions that will help me in my future
studies.
88
Achievements
Publications
First author publication:
[1].Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda. Pib2 is a cysteine sensor
involved in TORC1 activation. 投稿中.
[2]. Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda. TORC1 represses SER3
expression by inducing lncRNA SRG1 transcriptional interference. 投稿準備中
[3]. Zhang, H.-T., Zeng, Q., Wu, B., Lu, J., Tong, K.-L., Lin, J., Liu, Q.-Y., Xu, L.,
Yang, J., Liu, X., et al. (2021). TRIM21-regulated Annexin A2 plasma membrane
trafficking facilitates osteosarcoma cell differentiation through the TFEB-mediated
autophagy. Cell Death Dis. 12, 21. 10.1038/s41419-020-03364-2. (Co-first author)
[4]. Zeng, Q., Liu, W.T., Lu, J.L., Liu, X.H., Zhang, Y.F., Liu, L.X., and Gao, X.J.
(2018). YWHAZ Binds to TRIM21 but Is Not Involved in TRIM21-stimulated
Osteosarcoma Cell Proliferation. Biomed. Environ. Sci. BES 31, 186–196.
10.3967/bes2018.024.
Co-author publication:
89
[1]. Xu, G.-S., Lin, Y.-N., Zeng, Q., Li, Z.-P., Xiao, T., Ye, Y.-S., Li, Z.-Y., and Gao,
X. HSP90-regulated CHIP/TRIM21/p21 Axis Involves in the Senescence of
Osteosarcoma Cells. Protein Pept. Lett. 30, 1–7.
[2]. Si, H.W., Mei, X.F., Zeng, Q., Hui, L.X., Juan, G.X., and Xia, L.L. (2017).
ERK1/2-mediated Cytoplasmic Accumulation of hnRNPK Antagonizes TRAILinduced Apoptosis through Upregulation of XIAP in H1299 Cells. Biomed. Environ.
Sci. 30, 473–481. 10.3967/bes2017.063.
[3]. Gao, X., Xu, F., Zhang, H.-T., Chen, M., Huang, W., Zhang, Q., Zeng, Q., and Liu,
L. (2016). PKCα–GSK3β–NF-κB signaling pathway and the possible involvement of
TRIM21 in TRAIL-induced apoptosis. Biochem. Cell Biol. 94, 256–264. 10.1139/bcb2016-0009.
[4]. Huang CQ, Li W, Wu B, Chen WM, Chen LH, Mo GW, Zhang QF, Gong L, Li J,
Zhang HC, Zhu HM, Zeng Q. (2016). Pheretima aspergillum decoction suppresses
inflammation and relieves asthma in a mouse model of bronchial asthma by NF-κB
inhibition. J. Ethnopharmacol. 189, 22–30. 10.1016/j.jep.2016.05.028.
Conference Presentation
Qingzhong Zeng、荒木保弘、野田健司. 二つの TORC1 活性化経路の上流に位置
するアミノ酸の同定. 第 11 回 TOR 研究会. (2021/7/15-16)
90
Qingzhong Zeng、荒木保弘、野田健司. オートファジーを抑制する TORC1 の活
性化経路の上流に位置するアミノ酸の同定. 「マルチモードオートファジー」
第 3 回班会議・第 14 回オートファジー研究会. (2021/10/24-27)
Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda. TORC1 senses amino acids through
distinct upstream pathways to inhibit autophagy. The 10th International Symposium on
Autophagy. (2022/10/23-27)
Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda. Cysteine-activated TORC1 is
dependent on the Pib2 pathway in Saccharomyces cerevisiae. 第 12 回 TOR 研究会.
(2022/10/29-30)
Qingzhong Zeng, Yasuhiro Araki, Takeshi Noda. Cysteine-activated TORC1 is
dependent on the Pib2 pathway. The 45th Annual Meeting of the Molecular Biology
Society of Japan. (2022/11/30-12/2)
91
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