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. 2013 Nov 21;52(4):495-505.
doi: 10.1016/j.molcel.2013.09.016. Epub 2013 Oct 3.

The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1

Zhi-Yang Tsun  1   2 , Liron Bar-Peled #  1   2 , Lynne Chantranupong #  1   2 , Roberto Zoncu  1   2 , Tim Wang  1   2 , Choah Kim  1   2 , Eric Spooner  1 , David M Sabatini  1   2   3
Affiliations

The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1

Zhi-Yang Tsun et al. Mol Cell. .

Abstract

The mTORC1 kinase is a master growth regulator that senses numerous environmental cues, including amino acids. The Rag GTPases interact with mTORC1 and signal amino acid sufficiency by promoting the translocation of mTORC1 to the lysosomal surface, its site of activation. The Rags are unusual GTPases in that they function as obligate heterodimers, which consist of RagA or B bound to RagC or D. While the loading of RagA/B with GTP initiates amino acid signaling to mTORC1, the role of RagC/D is unknown. Here, we show that RagC/D is a key regulator of the interaction of mTORC1 with the Rag heterodimer and that, unexpectedly, RagC/D must be GDP bound for the interaction to occur. We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. Thus, we reveal a role for RagC/D in mTORC1 activation and a molecular function for the FLCN tumor suppressor.

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Figures

Figure 1
Figure 1. The RagC Nucleotide State Determines mTORC1 Binding to the Rag Heterodimer and Regulates Amino Acid Sensing by mTORC1
(A) Rag heterodimers containing RagCS75N co-immunoprecipitate the largest amount of endogenous mTORC1. Anti-FLAG immunoprecipitates were prepared from HEK-293T cells expressing the indicated cDNAs. Cell lysates and immunoprecipitates were analyzed by immunoblotting for the indicated proteins. (B) Raptor preferentially binds a GDP-loaded Rag heterodimer. In vitro binding assay in which recombinant HA-GST-tagged-RagB-RagC or -Rap2A were loaded with the indicated nucleotide and incubated with purified FLAG-tagged raptor protein. HA-GST precipitates were analyzed by immunoblotting for indicated proteins. Irrelevant lanes were removed and indicated by a dashed line. (C) Raptor only binds to the RagBX-C heterodimer when RagC is GDP-loaded. In vitro binding assay in which recombinant HA-GST-tagged-RagBX-RagC or -Rap2A were loaded with the indicated nucleotide and incubated with purified FLAG-tagged raptor protein and analyzed as in (B). (D) Raptor only binds to the RagB-CX heterodimer when RagCX is XDP-loaded. In vitro binding assay in which recombinant HA-GST-tagged-RagB-RagCX or -Rap2A were loaded with the indicated nucleotide and incubated with purified FLAG-tagged raptor protein and analyzed as in (B). (E) Expression of RagCS75N or RagCQ120L renders the mTORC1 pathway insensitive to amino acid levels. HEK-293T cells expresssing the indicated cDNAs were analyzed as in (A). Irrelevant lanes were removed and indicated by a dashed line.
Figure 2
Figure 2. FLCN-FNIP2 is a Rag-Interacting Complex and is Necessary for mTORC1 Activation by Amino Acids
(A) Recombinant epitope-tagged FLCN-FNIP2 co-immunoprecipitates endogenous RagA and RagC. Anti-FLAG immunoprecipitates were prepared from HEK-293T cells expressing the indicated cDNAs in expression vectors and analyzed along with cell lysates by immunoblotting for indicated proteins. Irrelevant lanes were removed and indicated by a dashed line. (B) Amino acid starvation increases the amount of endogenous FLCN that co-immunoprecipitates with recombinant RagB. HEK-293T cells stably expressing FLAG-RagB were starved for amino acids for 50 min, or starved and stimulated with amino acids for 10 min. Anti-FLAG immunoprecipitates were analyzed as in (A). (C) FLCN is necessary for the activation of the mTORC1 pathway by amino acids. HEK-293T cells expressing a control shRNA or two distinct shRNAs targeting FLCN were starved for amino acids for 50 min, or starved and stimulated with amino acids for 10 min. Levels of indicated proteins and phosphorylation states were analyzed by immunobloting of cell lysates. (D) FLCN function is conserved in Drosophila cells. Drosophila S2 cells were transfected with a control dsRNA, or dsRNAs targeting dRagB, or dFLCN, starved of amino acids for 90 min, or starved and re-stimulated with amino acids for 30 min and analyzed as in (C). (E) Knockdown of FLCN prevents amino acid-induced translocation of mTOR to lysosomes. HEK-293T cells expressing the indicated shRNAs were starved or starved and re-stimulated with amino acids for the specified times before co-immunostaining for mTOR (red) and LAMP2 (green). (F) FLCN is not required for the lysosomal localization of RagC. HEK-293T cells expressing the indicated shRNAs were treated and processed as described in (E). In all images, insets show selected fields that were magnified two times and their overlays. Scale bars represent 10 μm. See also Figure S1.
Figure 3
Figure 3. FLCN Localizes to the Lysosomal Surface in an Amino Acid-Sensitive Fashion
(A) FLCN localizes to the lysosomal surface. Spinning disk confocal image of a HEK-293T cell co-expressing FLCN-GFP, HA-FNIP2, and mRFP-LAMP1 (pseudo-colored red and green in merge, respectively). (B) FLCN associates with lysosomes as they traffic within cells. Time-lapse of FLCN- and LAMP1-positive lysosomes from the boxed region in (A) magnified by 2.5 times. Time intervals are in seconds. (C) FLCN localizes to the lysosomal surface upon amino acid starvation. HEK-293T cells expressing the indicated shRNAs were starved or starved and re-stimulated with amino acids for the specified times before co-immunostaining for FLCN (red) and LAMP2 (green). (D) Amino acid-sensitive localization of FLCN is independent of mTORC1 activity. HEK-293T cells treated with DMSO or Torin1 (250 nM) were starved or starved and re-stimulated with amino acids for the specified times before co-immunostaining for FLCN (red) and LAMP2 (green). In (C) and (D), insets show selected fields that were magnified two times and their overlays. All scale bars represent 10 μm. See also Movie S1 and Figure S2.
Figure 4
Figure 4. FLCN-FNIP is a GTPase-Activating Protein Complex for RagC and RagD
(A) Rag heterodimers containing RagBT54N, but not RagCS75N, co-immunoprecipitate endogenous FLCN. Anti-FLAG immunoprecipitates were prepared from HEK-293T cells transfected with indicated cDNAs in expression vectors. Cell lysates and immunoprecipitates were analyzed by immunoblotting of indicated proteins. (B) FLCN-FNIP stimulates GTP hydrolysis by RagC. 5 pmol of RagBQ99L-X-RagC was loaded with [α-32P]GTP and incubated with indicated proteins (20 pmol). GTP hydrolysis was determined by thin-layer chromatography (see Experimental Procedures). Each value represents the mean ± SD (n=3). (C) FLCN-FNIP stimulates GTP hydrolysis by RagD. GAP assay was performed with RagBQ99L-X RagD as described in (B). (D) GATOR1, but not FLCN-FNIP1/2, stimulates GTP hydrolysis by RagB. GAP assay was performed with RagB-RagCQ120L-X as described in (B). (E) FLCN-FNIP does not stimulate GTP hydrolysis by Rap2A. GAP assay was performed with the Rap2A control GTPase as described in (B). (F) Nucleotide state of RagB does not affect FLCN-FNIP2 GAP activity towards RagC, FLCNFNIP2 complex is required for GAP activity, and N-terminal region of FLCN is required for GAP activity. GAP assays were performed as described in (B) with 10 min incubations of indicated proteins. Values represent an average from at least 2 experiments. (G) FLCN-FNIP2 stimulates GTP hydrolysis by RagC in a dose-dependent manner. GAP assay was performed as described in (B) with indicated molar ratios of FLCN-FNIP2 or control metap2 to RagBX-RagC. (H) In vitro, the FLCN-FNIP2 GAP activity is sufficient to cause raptor to bind to the Rags. In vitro binding assay in which recombinant HA-GST-tagged-RagBX-RagC or -Rap2A were loaded with the indicated nucleotide and incubated with purified FLAG-tagged raptor along with FLCN-FNIP2 or metap2 control protein. HA-GST precipitates were analyzed by immunoblotting for indicated proteins. See also Figure S3.
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