Nutr Res Pract.  2009 Mar;3(1):64-71.

Mechanisms of amino acid sensing in mTOR signaling pathway

• Kim E

Abstract

Amino acids are fundamental nutrients for protein synthesis and cell growth (increase in cell size). Recently, many compelling evidences have shown that the level of amino acids is sensed by extra- or intra-cellular amino acids sensor(s) and regulates protein synthesis/degradation. Mammalian target of rapamycin complex 1 (mTORC1) is placed in a central position in cell growth regulation and dysregulation of mTOR signaling pathway has been implicated in many serious human diseases including cancer, diabetes, and tissue hypertrophy. Although amino acids are the most potent activator of mTORC1, how amino acids activate mTOR signaling pathway is still largely unknown. This is partly because of the diversity of amino acids themselves including structure and metabolism. In this review, current proposed amino acid sensing mechanisms to regulate mTORC1 and the evidences pro/against the proposed models are discussed.

Keyword

Amino acid signaling; mTOR; protein synthesis; cell growth

MeSH Terms

Amino Acids
Humans
Hypertrophy
Multiprotein Complexes
Sirolimus
TOR Serine-Threonine Kinases
Amino Acids
Multiprotein Complexes
Sirolimus
TOR Serine-Threonine Kinases

Figure

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  Fig. 1 Regulation of mTORC1 mTORC1 is a multiprotein complex composed of Raptor, mLST8, PRAS40, and FKBP38 and regulates protein synthesis and cell growth by phosphorylating S6K1 and 4EBP1. Rheb directly binds and activates mTOR kinase. GTP-bound active Rheb sequesters FKBP38 which otherwise binds and inhibits mTORC1. TSC1/2 heterodimer converts Rheb from GTP-bound active to GDP-bound inactive form. In Drosophila, TCTP was identified as Rheb GEF. mTORC1 activity is precisely coordinated by growth factors such as insulin or insulin-like growth factor and nutrients. Insulin binding to insulin receptor recruits IRS and subsequently activates PI3K and PDK1. PDK1 then phosphorylates and activates Akt which in turn phosphorylates two negative regulators of mTORC1, TSC2 and PRAS40, and relieves their inhibitory function. Amino acids stimulation does not phosphorylate Akt, however, strongly phosphorylates S6K and 4EBP1 in the absence of insulin stimulation. Recently three proteins, Rag, Vps34, and MAP4K3, have been presented as putative intracellular amino acid sensors. Each protein activates mTORC1 by distinctive mechanism. On the other hand, activated S6K1 phosphorylates and degrades IRS by negative feedback inhibition which in turn inhibits PI3K and mTORC1 signaling pathway (for details, see text). IRS: insulin receptor substrate; PI3K: phosphatidylinositol 3 phosphate kinase; PDK1: 3-phosphoinositide-dependent protein kinase1; Note: uncertain pathway is delineated as dashed line.

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  Fig. 2 Current proposed mechanisms of amino acid sensing by mTORC1 Amino acids are imported into the cells via various amino acid transporters and activate mTORC1 either by amino acid metabolites or by undefined membrane/intracellular amino acid sensor(s). Figure depicts a case of L-leucine (for details, see text). AT: aminotransferase; α-KIC: α-ketoisocaproic acid; BCKDH: branched-chain α-ketoacid dehydrogenase; GDH: glutamate dehydrogenase; AOAA: aminooxyacetic acid

Reference

1. Abraham RT, Wiederrecht GJ. Immunopharmacology of rapamycin. Annu Rev Immunol. 1996. 14:483–510.

2. Backer JM. The regulation and function of Class III PI3Ks: novel roles for Vps34. Biochem J. 2008. 410:1–17.

3. Bai X, Ma D, Liu A, Shen X, Wang QJ, Liu Y, Jiang Y. Rheb activates mTOR by antagonizing its endogenous inhibitor, FKBP38. Science. 2007. 318:977–980.

4. Balage M, Sinaud S, Prod'homme M, Dardevet D, Vary TC, Kimball SR, Jefferson LS, Grizard J. Amino acids and insulin are both required to regulate assembly of the eIF4E. eIF4G complex in rat skeletal muscle. Am J Physiol. 2001. 281:E565–E574.

5. Blommaart EF, Luiken JJ, Blommaart PJ, van Woerkom GM, Meijer AJ. Phosphorylation of ribosomal protein S6 is inhibitory for autophagy in isolated rat hepatocytes. J Biol Chem. 1995. 270:2320–2326.

6. Brown EJ, Albers MW, Shin TB, Ichikawa K, Keith CT, Lane WS, Schreiber SL. A mammalian protein targeted by G1-arresting rapamycin-receptor complex. Nature. 1994. 369:756–758.

7. Byfield MP, Murray JT, Backer JM. hVps34 is a nutrient-regulated lipid kinase required for activation of p70 S6 kinase. J Biol Chem. 2005. 280:33076–33082.

8. Chiu MI, Katz H, Berlin V. RAPT1, a mammalian homolog of yeast Tor, interacts with the FKBP12/rapamycin complex. Proc Natl Acad Sci U S A. 1994. 91:12574–12578.

9. Cruz MC, Cavallo LM, Gorlach JM, Cox G, Perfect JR, Cardenas ME, Heitman J. Rapamycin antifungal action is mediated via conserved complexes with FKBP12 and TOR kinase homologs in Cryptococcus neoformans. Mol Cell Biol. 1999. 19:4101–4112.

10. Dennis PB, Jaeschke A, Saitoh M, Fowler B, Kozma SC, Thomas G. Mammalian TOR: a homeostatic ATP sensor. Science. 2001. 294:1102–1105.

11. Dubouloz F, Deloche O, Wanke V, Cameroni E, De Virgilio C. The TOR and EGO protein complexes orchestrate microautophagy in yeast. Mol Cell. 2005. 19:15–26.

12. Facchinetti V, Ouyang W, Wei H, Soto N, Lazorchak A, Gould C, Lowry C, Newton AC, Mao Y, Miao RQ, Sessa WC, Qin J, Zhang P, Su B, Jacinto E. The mammalian target of rapamycin complex 2 controls folding and stability of Akt and protein kinase C. EMBO J. 2008. 27:1932–1943.

13. Fahien LA, MacDonald MJ, Kmiotek EH, Mertz RJ, Fahien CM. Regulation of insulin release by factors that also modify glutamate dehydrogenase. J Biol Chem. 1988. 263:13610–13614.

14. Findlay GM, Yan L, Procter J, Mieulet V, Lamb RF. A MAP4 kinase related to Ste20 is a nutrient-sensitive regulator of mTOR signalling. Biochem J. 2007. 403:13–20.

15. Fingar DC, Salama S, Tsou C, Harlow E, Blenis J. Mammalian cell size is controlled by mTOR and its downstream targets S6K1 and 4EBP1/eIF4E. Genes Dev. 2002. 16:1472–1487.

16. Gao M, Kaiser CA. A conserved GTPase-containing complex is required for intracellular sorting of the general amino-acid permease in yeast. Nat Cell Biol. 2006. 8:657–667.

17. Garami A, Zwartkruis FJ, Nobukuni T, Joaquin M, Roccio M, Stocker H, Kozma SC, Hafen E, Bos JL, Thomas G. Insulin activation of Rheb, a mediator of mTOR/S6K/4E-BP signaling, is inhibited by TSC1 and 2. Mol Cell. 2003. 11:1457–1466.

18. Garcia-Martinez JM, Alessi DR. mTOR complex 2 (mTORC2) controls hydrophobic motif phosphorylation and activation of serum- and glucocorticoid-induced protein kinase 1 (SGK1). Biocheml J. 2008. 416:375–385.

19. Garlick PJ, Grant I. Amino acid infusion increases the sensitivity of muscle protein synthesis in vivo to insulin. Effect of branched-chain amino acids. Biochem J. 1988. 254:579–584.

20. Guertin DA, Stevens DM, Thoreen CC, Burds AA, Kalaany NY, Moffat J, Brown M, Fitzgerald KJ, Sabatini DM. Ablation in mice of the mTORC components raptor, rictor, or mLST8 reveals that mTORC2 is required for signaling to Akt-FOXO and PKCalpha, but not S6K1. Dev Cell. 2006. 11:859–871.

21. Guertin DA, Sabatini DM. Defining the role of mTOR in cancer. Cancer cell. 2007. 12:9–22.

22. Gulati P, Gaspers LD, Dann SG, Joaquin M, Nobukuni T, Natt F, Kozma SC, Thomas AP, Thomas G. Amino acids activate mTOR complex 1 via Ca2+/CaM signaling to hVps34. Cell Metab. 2008. 7:456–465.

23. Hall DJ, Grewal SS, de la Cruz AF, Edgar BA. Rheb-TOR signaling promotes protein synthesis, but not glucose or amino acid import, in Drosophila. BMC Biol. 2007. 5:10.

24. Hara K, Maruki Y, Long X, Yoshino K, Oshiro N, Hidayat S, Tokunaga C, Avruch J, Yonezawa K. Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell. 2002. 110:177–189.

25. Hara K, Yonezawa K, Weng QP, Kozlowski MT, Belham C, Avruch J. Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism. J Biol Chem. 1998. 273:14484–14494.

26. Haussinger D. The role of cellular hydration in the regulation of cell function. Biochem J. 1996. 313:697–710.

27. Hay N, Sonenberg N. Upstream and downstream of mTOR. Genes Dev. 2004. 18:1926–1945.

28. Heitman J, Movva NR, Hall MN. Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science. 1991. 253:905–909.

29. Hsu YC, Chern JJ, Cai Y, Liu M, Choi KW. Drosophila TCTP is essential for growth and proliferation through regulation of dRheb GTPase. Nature. 2007. 445:785–788.

30. Hyde R, Taylor PM, Hundal HS. Amino acid transporters: roles in amino acid sensing and signalling in animal cells. Biochem J. 2003. 373:1–18.

31. Iiboshi Y, Papst PJ, Kawasome H, Hosoi H, Abraham RT, Houghton PJ, Terada N. Amino acid-dependent control of p70(s6k). Involvement of tRNA aminoacylation in the regulation. J Biol Chem. 1999. 274:1092–1099.

32. Ikenoue T, Inoki K, Yang Q, Zhou X, Guan KL. Essential function of TORC2 in PKC and Akt turn motif phosphorylation, maturation and signalling. EMBO J. 2008. 27:1919–1931.

33. Inoki K, Corradetti MN, Guan KL. Dysregulation of the TSC-mTOR pathway in human disease. Nat Gene. 2005b. 37:19–24.

34. Inoki K, Li Y, Xu T, Guan KL. Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling. Genes Dev. 2003a. 17:1829–1834.

35. Inoki K, Ouyang H, Li Y, Guan KL. Signaling by target of rapamycin proteins in cell growth control. Microbiol Mol Biol Rev. 2005a. 69:79–100.

36. Inoki K, Zhu T, Guan KL. TSC2 mediates cellular energy response to control cell growth and survival. Cell. 2003b. 115:577–590.

37. Jacinto E, Loewith R, Schmidt A, Lin S, Ruegg MA, Hall A, Hall MN. Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive. Nat Cell Biol. 2004. 6:1122–1128.

38. Juhasz G, Hill JH, Yan Y, Sass M, Baehrecke EH, Backer JM, Neufeld TP. The class III PI(3)K Vps34 promotes autophagy and endocytosis but not TOR signaling in Drosophila. J Cell Biol. 2008. 181:655–666.

39. Kim DH, Sarbassov DD, Ali SM, King JE, Latek RR, Erdjument-Bromage H, Tempst P, Sabatini DM. mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell. 2002. 110:163–175.

40. Kim DH, Sarbassov DD, Ali SM, Latek RR, Guntur KV, Erdjument-Bromage H, Tempst P, Sabatini DM. GbetaL, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. Mol Cell. 2003. 11:895–904.

41. Kim E, Goraksha-Hicks P, Li L, Neufeld TP, Guan KL. Regulation of TORC1 by Rag GTPases in nutrient response. Nat Cell Biol. 2008. 10:935–945.

42. Kim E, Guan KL. RAG GTPases in nutrient-mediated TOR signaling pathway. Cell Cycle. 2009. 8:[in publication].

43. Lee CH, Inoki K, Guan KL. mTOR pathway as a target in tissue hypertrophy. Annu Rev Pharmacol Toxicol. 2007. 47:443–467.

44. Lindmo K, Stenmark H. Regulation of membrane traffic by phosphoinositide 3-kinases. J Cell Sci. 2006. 119:605–614.

45. Loewith R, Jacinto E, Wullschleger S, Lorberg A, Crespo JL, Bonenfant D, Oppliger W, Jenoe P, Hall MN. Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol Cell. 2002. 10:457–468.

46. Long W, Saffer L, Wei L, Barrett EJ. Amino acids regulate skeletal muscle PHAS-I and p70 S6-kinase phosphorylation independently of insulin. Am J Physiol. 2000. 279:E301–E306.

47. Long X, Lin Y, Ortiz-Vega S, Yonezawa K, Avruch J. Rheb binds and regulates the mTOR kinase. Curr Biol. 2005a. 15:702–713.

48. Long X, Ortiz-Vega S, Lin Y, Avruch J. Rheb binding to mammalian target of rapamycin (mTOR) is regulated by amino acid sufficiency. J Biol Chem. 2005b. 280:23433–23436.

49. Lynch CJ, Fox HL, Vary TC, Jefferson LS, Kimball SR. Regulation of amino acid-sensitive TOR signaling by leucine analogues in adipocytes. J Cell Biochem. 2000. 77:234–251.

50. May ME, Buse MG. Effects of branched-chain amino acids on protein turnover. Diabetes Metabol Rev. 1989. 5:227–245.

51. McDaniel ML, Marshall CA, Pappan KL, Kwon G. Metabolic and autocrine regulation of the mammalian target of rapamycin by pancreatic beta-cells. Diabetes. 2002. 51:2877–2885.

52. Menand B, Desnos T, Nussaume L, Berger F, Bouchez D, Meyer C, Robaglia C. Expression and disruption of the Arabidopsis TOR (target of rapamycin) gene. Proc Natl Acad Sci U S A. 2002. 99:6422–6427.

53. Miotto G, Venerando R, Khurana KK, Siliprandi N, Mortimore GE. Control of hepatic proteolysis by leucine and isovaleryl-L-carnitine through a common locus. Evidence for a possible mechanism of recognition at the plasma membrane. J Biol Chem. 1992. 267:22066–22072.

54. Miotto G, Venerando R, Marin O, Siliprandi N, Mortimore GE. Inhibition of macroautophagy and proteolysis in the isolated rat hepatocyte by a nontransportable derivative of the multiple antigen peptide Leu8-Lys4-Lys2-Lys-beta Ala. J Biol Chem. 1994. 269:25348–25353.

55. Nicklin P, Bergman P, Zhang B, Triantafellow E, Wang H, Nyfeler B, Yang H, Hild M, Kung C, Wilson C, Myer VE, MacKeigan JP, Porter JA, Wang YK, Cantley LC, Finan PM, Murphy LO. Bidirectional transport of amino acids regulates mTOR and autophagy. Cell. 2009. 136:521–534.

56. Nobukuni T, Joaquin M, Roccio M, Dann SG, Kim SY, Gulati P, Byfield MP, Backer JM, Natt F, Bos JL, Zwartkruis FJ, Thomas G. Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase. Proc Natl Acad Sci U S A. 2005. 102:14238–14243.

57. Nobukuni T, Kozma SC, Thomas G. hvps34, an ancient player, enters a growing game: mTOR Complex1/S6K1 signaling. Curr Opin Cell Biol. 2007. 19:135–141.

58. Odorizzi G, Babst M, Emr SD. Phosphoinositide signaling and the regulation of membrane trafficking in yeast. Trends Biochem Sci. 2000. 25:229–235.

59. Oldham S, Montagne J, Radimerski T, Thomas G, Hafen E. Genetic and biochemical characterization of dTOR, the Drosophila homolog of the target of rapamycin. Genes Dev. 2000. 14:2689–2694.

60. Oshiro N, Takahashi R, Yoshino K, Tanimura K, Nakashima A, Eguchi S, Miyamoto T, Hara K, Takehana K, Avruch J, Kikkawa U, Yonezawa K. The proline-rich Akt substrate of 40 kDa (PRAS40) is a physiological substrate of mammalian target of rapamycin complex 1. J Biol Chem. 2007. 282:20329–20339.

61. Pearce LR, Huang X, Boudeau J, Pawlowski R, Wullschleger S, Deak M, Ibrahim AF, Gourlay R, Magnuson MA, Alessi DR. Identification of Protor as a novel Rictor-binding component of mTOR complex-2. Biochem J. 2007. 405:513–522.

62. Redpath NT, Foulstone EJ, Proud CG. Regulation of translation elongation factor-2 by insulin via a rapamycin-sensitive signalling pathway. EMBO J. 1996. 15:2291–2297.

63. Roccio M, Bos JL, Zwartkruis FJ. Regulation of the small GTPase Rheb by amino acids. Oncogene. 2006. 25:657–664.

64. Sabatini DM, Erdjument-Bromage H, Lui M, Tempst P, Snyder SH. RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs. Cell. 1994. 78:35–43.

65. Sancak Y, Thoreen CC, Peterson TR, Lindquist RA, Kang SA, Spooner E, Carr SA, Sabatini DM. PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase. Mol Cell. 2007. 25:903–915.

66. Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science. 2008. 320:1496–1501.

67. Sarbassov DD, Ali SM, Kim DH, Guertin DA, Latek RR, Erdjument-Bromage H, Tempst P, Sabatini DM. Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr Biol. 2004. 14:1296–1302.

68. Saucedo LJ, Gao X, Chiarelli DA, Li L, Pan D, Edgar BA. Rheb promotes cell growth as a component of the insulin/TOR signalling network. Nat Cell Biol. 2003. 5:566–571.

69. Schmelzle T, Hall MN. TOR, a central controller of cell growth. Cell. 2000. 103:253–262.

70. Sener A, Malaisse WJ. L-leucine and a nonmetabolized analogue activate pancreatic islet glutamate dehydrogenase. Nature. 1980. 288:187–189.

71. Shah OJ, Anthony JC, Kimball SR, Jefferson LS. 4E-BP1 and S6K1: translational integration sites for nutritional and hormonal information in muscle. Am J Physiol. 2000. 279:E715–E729.

72. Shintani T, Klionsky DJ. Autophagy in health and disease: a double-edged sword. Science. 2004. 306:990–995.

73. Smith EM, Finn SG, Tee AR, Browne GJ, Proud CG. The tuberous sclerosis protein TSC2 is not required for the regulation of the mammalian target of rapamycin by amino acids and certain cellular stresses. J Biol Chem. 2005. 280:18717–18727.

74. Tee AR, Manning BD, Roux PP, Cantley LC, Blenis J. Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb. Curr Biol. 2003. 13:1259–1268.

75. Vander Haar E, Lee SI, Bandhakavi S, Griffin TJ, Kim DH. Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nat Cell Biol. 2007. 9:316–323.

76. Wang L, Harris TE, Roth RA, Lawrence JC Jr. PRAS40 regulates mTORC1 kinase activity by functioning as a direct inhibitor of substrate binding. J Biol Chem. 2007. 282:20036–20044.

77. Xu G, Kwon G, Cruz WS, Marshall CA, McDaniel ML. Metabolic regulation by leucine of translation initiation through the mTOR-signaling pathway by pancreatic beta-cells. Diabetes. 2001. 50:353–360.

78. Yan Y, Backer JM. Regulation of class III (Vps34) PI3Ks. Biochem Soc Trans. 2007. 35:239–241.

79. Yan Y, Flinn RJ, Wu H, Schnur RS, Backer JM. hVps15, but not Ca(2+)/CaM, is required for the activity and regulation of hVps34 in mammalian cells. Biochem J. 2009. 417:747–755.

80. Yang Q, Guan KL. Expanding mTOR signaling. Cell Res. 2007. 17:666–681.

81. Zhang Y, Gao X, Saucedo LJ, Ru B, Edgar BA, Pan D. Rheb is a direct target of the tuberous sclerosis tumour suppressor proteins. Nat Cell Biol. 2003. 5:578–581.