Amino acid signaling to mTOR mediated by inositol polyphosphate multikinase

Abstract

mTOR complex 1 (mTORC1; mammalian target of rapamycin [mTOR] in complex with raptor) is a key regulator of protein synthesis and cell growth in response to nutrient amino acids. Here we report that inositol polyphosphate multikinase (IPMK), which possesses both inositol phosphate kinase and lipid kinase activities, regulates amino acid signaling to mTORC1. This regulation is independent of IPMK's catalytic function, instead reflecting its binding with mTOR and raptor, which maintains the mTOR-raptor association. Thus, IPMK appears to be a physiologic mTOR cofactor, serving as a determinant of mTORC1 stability and amino acid-induced mTOR signaling. Substances that block IPMK-mTORC1 binding may afford therapeutic benefit in nutrient amino acid-regulated conditions such as obesity and diabetes.

Figure 1. IPMK depletion diminishes amino acid signaling and mTOR-raptor interactions

(A) Wild-type (WT) and IPMK-depleted (KO) MEFs were grown in 10% serum, nutrient-rich medium (control), deprived of serum and amino acids (leucine, arginine, or total amino acids) for 1 hour. Cells were stimulated by leucine (400 μM), arginine (400 μM), or total amino acids mixture (1×) for 10 min. (B) In vitro mTORC1 activity assay from leucine-treated MEFs. (C) MEFs were deprived of leucine for 24 hours and stimulated with leucine (400 μM) for 12 hours. Cell size was analyzed from at least 8,000 cells per trial (n = 3). Bars represent mean ± SEM. (D) IPMK-depleted MEFs stably expressing wild-type or the catalytically inactive, mutant IPMK (K129A) were analyzed as in (A). (E) mTOR, raptor, and rictor immunoprecipitates were isolated in the presence of DSP, and the amount of indicated mTORC subunits were analyzed. Bars in (A), (B), and (E) represent mean ± SD (n = 4). **p < 0.01.

Figure 2. IPMK is an mTOR-associated protein

(A) GST or GST-hIPMK was expressed in HEK293T cells, followed by pulldown and immunoblotting for endogenous mTOR. (B) GFP or GFP-hIPMK was co-transfected in HEK293T cells with myc-mTOR, and immunoprecipitates were analyzed by immunoblotting. (C) Lysates from IPMK-depleted MEFs stably expressing wild-type mouse IPMK were immunoprecipitated with indicated antibodies. (D) The unique sequence found in mammalian IPMK is aligned and indicated with a red box. Yeast IPMK-specific, polyaspartates sequence (Poly-D; green) and two conserved domains for inositol binding (blue) and kinase activity (yellow) are shown. IPMK fragments used for binding studies are shown in the schematic with the number of the amino acid sequence. (E) HA-mTOR or HA-raptor was co-transfected in HEK293T cells with wild-type or 1–60 deleted human IPMK (Δ1–60) constructs, followed by immunoprecipitation with HA-antibodies and immunoblotting. (F) Myc-wild-type mTOR, 1–1482 (N-ter) fragment, or 1328–2549 (C-ter) fragment was co-transfected in HEK293T cells with GFP or GFP-hIPMK-1–60, and myc-immunoprecipitates were analyzed by immunoblotting. (G) GST or GST-hIPMK-1–60 was incubated with mTOR purified from HEK293T cells. (H) GST or GST-hIPMK was co-transfected in HEK293T cells with myc-raptor, and myc-immunoprecipitates were analyzed by immunoblotting.

Figure 3. Human IPMK-1–60 peptide interferes with mTOR-raptor binding and amino acid signaling

(A) HEK293T cells transfected with GFP or GFP-hIPMK-1–60 were deprived of serum and leucine for 1 hour, and stimulated with leucine for 10 min. mTORC1 and mTORC2 were isolated in the presence of DSP, and the amount of mTOR was analyzed. (B) S6K phosphorylation and protein expression were analyzed by immunoblotting. (C) The amount of myc-raptor bound in mTOR pulldown and in vitro mTORC1 activity were analyzed. mTOR immunopurified from leucine-treated HEK293T cells and myc-raptor (100 nM) were co-incubated with GST or GST-hIPMK-1–60 (200 nM). Bars represent mean ± SD (n = 3 in A and C, n = 4 in B). *p < 0.05; **p < 0.01.

Figure 4. The amino-terminus of IPMK is involved in mTOR-raptor binding and amino acid signaling

(A) In the presence of DSP, raptor immunoprecipitates were isolated from IPMK-depleted MEFs stably expressing vector (Vec), wild-type (WT), or the deletion mutant IPMK (Δ1–31) followed by immunoblotting. (B) S6K phosphorylation and protein expression were analyzed by immunoblotting. Bars represent mean ± SD (n = 3). *p < 0.05; **p < 0.01. (C) A model depicting regulation of mTORC1 signaling by IPMK in response to amino acids. In the absence of amino acids IPMK binds with high affinity to mTORC1, the N-terminal portion of IPMK interacting with mTOR and the C-terminus with raptor. Amino acid stimulation transforms the complex into a low affinity state, whereupon the complex translocates to the lysosomal surface. The active Rag/Regulator complex associates with raptor, and active GTP-Rheb binds to mTOR thereby enhancing mTOR activity (Sancak et al., 2010). In the absence of IPMK the mTOR-raptor complex dissociates, at least partially. Amino acid treatment still enhances raptor binding to the active Rag/Regulator complex, but GTP-Rheb fails to bind/activate mTOR.