Structure of the nutrient-sensing hub GATOR2

Abstract

Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients^1,2. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively^3-5. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1 MDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 β-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and α-solenoids. Integration of SEH1L and SEC13 into the scaffold through β-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes⁶. The scaffold orients the WD40 β-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway.

Extended Data Figure 1:. GATOR2 integrity and composition are insensitive to amino acid availability

(a) Amino acids do not regulate the size of the GATOR2 complex. Elution fractions from size-exclusion chromatography of transfected GATOR2 or endogenously-tagged GATOR2 were analyzed by SDS-PAGE. Gels were stained with Coomassie Blue or SYPRO Ruby, as indicated. n.s. indicates a non-specific co-purifying contaminant. Lane labels indicate elution volumes from TSKgel G4000SWxl column. (b) Analyses of endogenously tagged-WDR59 and -DEPDC5 expression in cell lysates. (c) Analysis of mTORC1 signaling in cell lysates from which endogenously-tagged GATOR2 was purified in (a). (d) Amino acids do not regulate the subunit composition or stoichiometry of endogenous GATOR2. Peak elution fractions from size-exclusion chromatography of endogenously-tagged GATOR2 were analyzed by SDS-PAGE and the gel was stained with SYPRO Ruby. (e) The subunit composition of GATOR2 and the interaction between GATOR2 and GATOR1 or KICSTOR are not regulated by amino acids. Anti-FLAG immunoprecipitates were prepared from HEK293T cells with the indicated genotype and were analyzed by immunoblotting for the indicated proteins. Data in (a)-(e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 2:. Modular Architecture of GATOR2

(a) Two orthogonal views of the molecular model of GATOR2. (b), (c), (d) Molecular models (top) and corresponding domain schematics (bottom) of three distinct building blocks of GATOR2: MIOS-SEH1L (b), WDR24-SEH1L (c), and WDR59-SEC13 (d). Domains not resolved in our cryo-EM structure are drawn with increased transparency for reference. (e) Each core GATOR2 subunit (MIOS, WDR24, WDR59) associates with either SEH1L or SEC13. Anti-FLAG immunoprecipitates were prepared from HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. HA, hemagglutinin. Data in (e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 3:. Surface properties of GATOR2

a) Three orthogonal views of GATOR2 are shown in surface representation and colored by: subunit identity (top), molecular lipophilicity potential (middle), coulombic electrostatic potential (bottom). Surface calculations were performed in ChimeraX, with atomic lipophilicity values from Ghose et al. The most lipophilic surfaces are drawn as orange and the least lipophilic as cyan. Negatively charged surfaces are drawn as red, and positively as blue. GATOR2 is highly charged at its surface, with the only exposed lipophilic patches of significant size found near the donor β-blade of WDR59, and the β-propeller of WDR24 (see panels (b) and (c) for details). Furthermore, there are two major surface patches where either negative or positive charge dominates. The mostly-positive patch stretches from the side of the β-propeller of WDR24, through the WDR24-MIOS CTD, to MIOS glove β-propeller. The mostly-negative patch starts with the MIOS α-solenoid, passes through the MIOS-WDR59 CTD, and ends at the tip of SEC13. The center of MIOS β-propellers appears highly positively charged. (b) Detailed view of the lipophilic patch near the donor β-blade of WDR59. While it might appear that the surface of the WDR59 β-blade forms a lipophilic groove, that groove is in fact occupied by protein density extending from the α-solenoid of WDR24. This WDR24 density likely continues to the top of the SEC13^WDR59 β-propeller (green dashed line), where we found two better-resolved stretches of amino-acid sequence (colored in gray). Yet, for these particular sections of GATOR2, we were unable to build a high-confidence structural model or to unambiguously deduce the amino-acid sequence. (c) Detailed view of the highly lipophilic and charged surface of the WDR24 β-propeller. The WDR24 β-propeller contains strong patches of negatively and positively charged surface. There are additional sporadic sections of highly lipophilic surface. Residues predicted by the DREAMM algorithm as membrane-penetrating are drawn as spheres.

Extended Data Figure 4:. GATOR2 CTDs contain RING domains

(a) Sequence alignment of the homologous C-terminal regions of MIOS, WDR24, and WDR59. Zinc-coordinating residues are highlighted in yellow. Zinc-coordinating residues in the ZnF are indicated by red dots. Zinc-coordinating residues in the RING domain are indicated with blue dots. (b) Side-by-side comparison of the structurally-aligned MIOS, WDR24, and WDR59 CTDs. (c) Structural comparison of the MIOS, WDR24, and WDR59 RING domains with the E3 ligase RNF4 RING domain (PDB ID: 4AP4). (d), (e), and (f) Detailed views of the experimental map and the corresponding molecular model surrounding the zinc coordination sites within the MIOS CTD ZnF (d) and RING domain, (e) and (f). (g) Schematic of zinc ion coordination in the MIOS CTD. The MIOS CTD coordinates a total of four zinc ions with 15 amino-acid side chains — similarly to the CTDs in WDR24 and WDR59. (h) Cartoon representation of the zinc ion coordination in a canonical RING domain associated with E3 ubiquitin ligase activity. The RING domain coordinates two zinc ions with eight side chains.

Extended Data Figure 5:. CTD-CTD junctions link core GATOR2 proteins

(a) Structural comparison (top) and schematic representations (bottom) of the MIOS-WDR24 and MIOS-WDR59 CTD-CTD junctions. Auxiliary interactions between CTDs and SEH1L or SEC13 contribute to the interface. This mode of interaction is distinct from that reported for dimeric RING E3 ligases^–. (b) View of the interface formed between the βC4 strands of the MIOS and WDR24 CTDs. Additional hydrophobic side chains from the MIOS and WDR24 βC1 strands, the MIOS αC2 helix and the WDR24 αC1 helix contribute to the interaction. (c) View of the interface formed between the βC4 strands of the MIOS and WDR59 CTDs. Additional hydrophobic side chains from the MIOS and WDR59 βC1 strands, the MIOS αC2 helix and the WDR59 αC1 helix contribute to the interaction. (d) The CTDs of MIOS and WDR59 are sufficient to mediate the MIOS-WDR59 interaction. Anti-FLAG immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. (e) The CTDs of MIOS and WDR24 are sufficient to mediate the MIOS-WDR24 interaction. Anti-FLAG immunoprecipitates were prepared from WDR59-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (f) The WDR24 CTD is necessary for the MIOS-WDR24 interaction. Anti-FLAG immunoprecipitates were prepared from WDR59-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (g) The MIOS CTD is necessary for the MIOS-WDR24 interaction. Anti-FLAG immunoprecipitates were prepared from WDR59-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (h) The WDR59 CTD is necessary for the MIOS-WDR59 interaction. Anti-FLAG immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (i) The MIOS CTD is necessary for the MIOS-WDR59 interaction. Anti-FLAG immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). Data in (d)-(i) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 6:. GATOR2 CTDs are required for complex assembly and function

(a) Size-exclusion chromatography profiles for wild-type GATOR2 (WT, black) or GATOR2 without individual CTDs: WDR24 CTD (WDR24 ∆CTD, green), WDR59 CTD (WDR59 ∆CTD, red), or MIOS CTD (MIOS ∆CTD, blue). The y-axis indicates normalized absorbance at 280 nm. Estimated molecular weights are indicated above each GATOR2 peak. (b) Elution fractions from size-exclusion chromatography of wild-type GATOR2 or GATOR2 without the MIOS CTD (MIOS ∆CTD), the WDR24 CTD (WDR24 ∆CTD), and the WDR59 CTD (WDR59 ∆CTD), corresponding to panel (a). The gel image of wild-type GATOR2 elution fractions was reproduced from Extended Data Fig. 1a. Lane labels indicate elution volume from TSKgel G4000SWxl column. (c), (d) The CTDs of WDR24 and WDR59 appear to be dispensable for the assembly of GATOR2 when analyzed by immunoprecipitation and immunoblotting. Anti-FLAG immunoprecipitates were prepared from WDR24-deficient (c) or WDR59-deficient (d) HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. (e) The MIOS CTD is required for MIOS to immunoprecipitate WDR24, WDR59 and SEC13. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (c). (f), (g), and (h) The CTDs of MIOS (f), WDR24 (g), and WDR59 (h) are necessary for mTORC1 activation and for the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from MIOS-deficient (f), WDR24-deficient (g), or WDR59-deficient (h) HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (c). HA, hemagglutinin. Data in (a)-(h) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 7:. GATOR2 RING domains are incompatible with E2 binding

Structural alignment between GATOR2 CTD-CTD junctions and the RNF4-UBCH5A complex (PDB ID: 4AP4). Individual CTD pairs are drawn (left) and superimposed with RNF4-UBCH5A (right) as follows: (a) WDR24-MIOS, (b) MIOS-WDR24, (c) MIOS-WDR59, and (d) WDR59-MIOS.

Extended Data Figure 8:. GATOR2 complex does not exhibit E3 ubiquitin ligase activity

(a), (b) In vitro ubiquitination assay does not demonstrate GATOR2-dependent ubiquitin chain formation or modification of GATOR1. GATOR1 (500 nM) was incubated with a panel of E2 enzymes in the absence (a) or presence of GATOR2 (250 nM; b). Reactions were incubated at 37°C for 1 h and analyzed by immunoblotting for the indicated proteins. (c) Coomassie-stained SDS-PAGE analysis of GATOR1 and GATOR2 complexes assayed in (a) and (b). (d) Ubiquitin chains formed in the presence of GATOR2 and UBE2D3 are not affected by GATOR2 inhibitors Sestrin2 or CASTOR1. UBE4B was used as a positive control for E3-dependent ubiquitin chain forming activity. Reactions were analyzed as in (a). (e) GATOR2 does not promote ubiquitin discharge from E2~Ub conjugates. Ubiquitin charged-UBE2D3 (UBE2D3~Ub) was incubated in the presence of 10 mM lysine and UBE4B, HOIP catalytic domain, or GATOR2 (100 nM each) at 22°C for the indicated amounts of time. Samples were harvested in SDS-PAGE buffer without reducing agent, except where otherwise indicated, to preserve the E2~Ub thioester linkage. (f) Pharmacological inhibition of the ubiquitination cascade does not affect activation of mTORC1 by amino acids. HEK293T cells were treated with 0.5 μM TAK-243 for a total of 4 h. Cells were starved of amino acids for 60 min and restimulated with amino acids for 15 min prior to harvest. Samples were harvested in SDS-PAGE sample buffer without reducing agent to preserve the E2~Ub thioester linkage and analyzed by immunoblotting. (g) NPRL2 lysine residues are not required for activation and regulation of mTORC1 by amino acids. NPRL2-deficient cells stably expressing the indicated constructs were starved of amino acids for 60 min and restimulated with amino acids for 15 min prior to harvest and were analyzed by immunoblotting for the indicated proteins. HA, hemagglutinin. (h) NPRL3 lysine residues are not required for activation and regulation of mTORC1 by amino acids. NPRL3-deficient cells stably expressing the indicated constructs were starved of amino acids for 60 min and restimulated with amino acids for 15 min prior to harvest and were analyzed as in (g). Data in (a), (b), (d)-(h) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 9:. WDR24-WDR59 α-solenoid junction is required for GATOR2 assembly and function

(a) Two views of the WDR24-WDR59 α-solenoid junction. (b) Mutations in the WDR24 α-solenoid domain disrupt the WDR24-WDR59 interaction. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. HA, hemagglutinin. (c) The WDR24-WDR59 interaction is required for activation of mTORC1 and the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (b). (d) Mutation of the WDR59 solenoidal domain disrupts the WDR24-WDR59 interaction. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (b). (e) The WDR24-WDR59 interaction is required for activation of mTORC1 and the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (b). Data in (b)-(e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 10:. MIOS-MIOS α-solenoid homodimerization is required for GATOR2 assembly and function

(a) Structure of the MIOS-MIOS α-solenoid junction. The two interacting MIOS protomers are colored as either darker (MIOS^A) or lighter blue (MIOS^B). (b) Mutagenesis of the interface between the two MIOS α-solenoids (MIOS A560E) disrupts MIOS homodimerization. Anti-FLAG immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. (c) Size-exclusion chromatography traces comparing the elution profile of GATOR2 containing wild-type MIOS with GATOR2 containing MIOS A560E. The trace for wild-type GATOR2 was reproduced from Extended Data Fig. 6a. (d) SDS-PAGE analysis of elution fractions from size-exclusion chromatography in (c). The gel image of wild-type GATOR2 elution fractions was reproduced from Extended Data Fig. 1a. Lane labels indicate elution volume from TSKgel G4000SWxl column. (e) Integrity of the MIOS α-solenoid junction is necessary for mTORC1 activation and the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (b). HA, hemagglutinin. Data in (b)-(e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 11:. Core GATOR2 proteins incorporate SEH1L and SEC13 by blade donation

(a) Structure (left) and schematic (right) of the SEH1L^WDR24 β-propeller completed by the donated WDR24 β-blade. (b) Structure (left) and schematic (right) of the SEH1L^MIOS β-propeller completed by the donated MIOS β-blade. (c) Structure (left) and schematic (right) of the SEC13^WDR59 β-propeller completed by the donated WDR59 β-blade. (d) Mutation of the donated WDR24 β-blade disrupts association of WDR24 with SEH1L. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. HA, hemagglutinin. (e) Mutation of the donated MIOS β-blade disrupts association of MIOS with SEH1L. Anti-FLAG immunoprecipitates were prepared from HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (f) Mutation of the donated WDR59 β-blade disrupts association of WDR59 with SEC13. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (d). (g) Depletion of SEH1L or SEC13 destabilizes GATOR2 proteins and disrupts complex formation. SEH1L or SEC13 were depleted by CRISPR/Cas9 in a HEK293T clone expressing endogenously tagged 3xFLAG-WDR59. Anti-FLAG immunoprecipitates were prepared and analyzed as in (d). (h), (i) Depletion of SEH1L (h) or SEC13 (i) renders mTORC1 signaling resistant to amino acid availability. HEK293T cells of the indicated genotype were starved of amino acids for 60 min and restimulated with amino acids for 15 min prior to harvest and analysis by immunoblotting. Data in (d)-(i) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Extended Data Figure 12:. Functional analysis of the core GATOR2 β-propellers

(a) The β-propellers of MIOS, WDR59, and WDR24 are required for interactions between GATOR2 and CASTOR1, GATOR1 and KICSTOR, and Sestrin2, respectively. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient, WDR59-deficient or WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. CASTOR1 D304A and Sestrin2 E451Q mutants do not bind arginine or leucine, respectively, and bind GATOR2 irrespective of amino acid availability. HA, hemagglutinin. (b) Schematic comparing WDR24 Nβ and SEH1L β-propeller organization in wild-type and β-single chain (βsc) constructs. (c) Schematic comparing WDR59 Nβ and SEC13 β-propeller organization in wild-type and β-single chain (βsc) constructs. The fused construct contains the intervening RWD domain. (d) The GATOR2 single chain β-propeller pairs of MIOS-SEH1L, WDR59-SEC13, and WDR24-SEH1L are sufficient to interact with CASTOR1, GATOR1 and KICSTOR, and Sestrin2, respectively. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (e) GATOR2 mediates the interaction between Sestrin2 and CASTOR1, indicating that they can co-occupy the same GATOR2 particle. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (f) Sestrin2 and CASTOR1, but not SAR1B, interact with GATOR2 and suppress mTORC1 signaling. Anti-FLAG and anti-HA immunoprecipitates were prepared from HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (g) GATOR2 interacts with Sestrin2 and CASTOR1, but not SAR1B. Anti-FLAG immunoprecipitates were prepared from HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (h) GATOR2 does not immunoprecipitate the Rag GTPases independent of GATOR1. Anti-FLAG immunoprecipitates were prepared from wild-type of DEPDC5-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (i) MIOS Nβ is not absolutely required for activation of mTORC1 or the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (j) WDR59 Nβ is necessary for activation of mTORC1 and the GATOR2-GATOR1 and GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from WDR59-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). Data in (a), (d)-(j) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Figure 1:. Structure of human GATOR2

(a) Size-exclusion chromatography profile of human GATOR2 used for structural analyses. mAU, milli-absorbance unit. (b) Coomassie Blue stained SDS-PAGE analysis of purified GATOR2. Asterisk indicates the CCT chaperonin complex that co-purifies with GATOR2. (c) Cryo-EM structure of the human GATOR2 complex. Two views of the experimental map (top) are shown next to the corresponding views of the molecular model (bottom). The C2 symmetry axis is perpendicular to the viewing plane, and marked with a filled ellipse. (d) Domain organization of GATOR2 components. Numbers denote the boundaries of the indicated domains. Gray trapezoids indicate β-blade donation by WDR24, MIOS, or WDR59 to complete β-propellers of SEH1L or SEC13. (e) Loss of core GATOR2 components renders mTORC1 signaling insensitive to amino acid availability. HEK293T cell clones of the indicated genotype were starved for amino acids for 60 min and restimulated with amino acids for 15 min prior to harvest. Cell lysates were analyzed by immunoblotting for the levels and phosphorylation states of the indicated proteins. Data in (e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Figure 2:. MIOS interacts with WDR24 and WDR59 via dimerization of C-terminal Zn-binding domains (CTDs)

(a) The GATOR2 octagonal scaffold contains four CTD-CTD junctions, supported by interactions with adjacent SEH1L and SEC13 β-propellers. (b) The CTDs of MIOS and WDR24 cross over one another and dimerize via a RING-RING interface, RING-solenoid interactions, and contacts between ZnFs and associated SEH1L propellers forming a “forearm shake,” as cartooned. (c) Two views of the molecular model of the WDR24-MIOS CTD-CTD junction. Each CTD coordinates four zinc ions: one in the ZnF and three in the RING. Zinc ions are colored teal. For a detailed representation of the MIOS CTD, see Extended Data Figure 4. (d) The MIOS CTD interacts with WDR24 and WDR59 CTDs. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. HA, hemagglutinin. Data in (d) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.

Figure 3:. α-solenoid junctions, supported by β-propellers of SEH1L and SEC13, complete the GATOR2 scaffold

(a) Four α-solenoid junctions, stabilized by adjacent SEH1L and SEC13 β-propellers, complete the GATOR2 scaffold. (b) Two views of the WDR24-WDR59 α-solenoid junction. The helical interface is supported by contacts between WDR59 and SEH1L^WDR24 and between WDR24 and SEC13^WDR59. For a detailed representation of the helical interface, see Extended Data Figure 9. (c) WDR24 completes SEH1L^WDR24 by β-blade donation. The incorporated SEH1L interacts with the WDR24 β-propeller, the WDR24 solenoidal domain, the WDR59 solenoidal domain, and the MIOS CTD. (d) Detailed view of the β-blade donation from WDR24 to complete SEH1L^WDR24. WDR24 contributes the three innermost strands of the seventh SEH1L propeller blade.

Figure 4:. The GATOR2 β-propellers receive and transmit amino acid availability

(a) The β-propellers of MIOS, WDR59, and WDR24 are required for the interactions of GATOR2 with CASTOR1, GATOR1 and KICSTOR, as well as Sestrin2, respectively. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient, WDR59-deficient or WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed by immunoblotting for the indicated proteins. CASTOR1 D304A and Sestrin2 E451Q mutants do not bind arginine or leucine, respectively, and bind GATOR2 irrespective of amino acid availability. HA, hemagglutinin. (b) Schematic comparing MIOS Nβ and SEH1L β-propeller organization in wild-type and β-single chain (βsc) constructs. (c) The GATOR2 single chain β-propeller pairs of MIOS-SEH1L, WDR59-SEC13, and WDR24-SEH1L are sufficient to interact with CASTOR1, GATOR1, and Sestrin2, respectively. Anti-FLAG immunoprecipitates were prepared from MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs and were analyzed as in (a). (d) MIOS Nβ is necessary for arginine deprivation, but not total amino acid deprivation, to inhibit mTORC1 signaling. MIOS-deficient HEK293T cells that transiently expressed the indicated cDNAs were starved of either all amino acids or arginine for 60 min and restimulated with amino acids or arginine for 15 min prior to harvest. Anti-HA immunoprecipitates were prepared and analyzed as in (a). (e) WDR24 Nβ is required for activation of mTORC1 but not for the GATOR2-GATOR1 or GATOR2-KICSTOR interactions. Anti-FLAG and anti-HA immunoprecipitates were prepared from WDR24-deficient HEK293T cells that transiently expressed the indicated cDNAs and analyzed as in (a). (f) Schematic of the integration of amino acid availability by GATOR2 β-propellers. The eye symbol indicates the viewing angle of GATOR2 in the bottom panel. The WDR59 Nβ was modeled using RoseTTAFold. Models for CASTOR1 (PDB ID: 5GT8), Sestrin2 (PDB ID: 5DJ4), and GATOR1 (PDB ID: 6CET) were obtained from the PDB. Data in (a), (c), (d), and (e) are representative of two independent experiments. For gel source data, see Supplementary Figure 1.