localization to control SLC38A9 or its regulators.
The fact that SLC38A9 also signals arginine levels
to mTORC1 (40–42) suggests that SLC38A9 is
part of a sophisticated system for coordinating
m TORC1 activity and lysosomal amino acid efflux
with the concentrations of cytosolic and lysosomal
amino acids. Our findings provide an example of
the utility of LysoIP for uncovering a new function for lysosomes—the sequestering of essential
amino acids upon m TORC1 inhibition. The method
that we described may be useful for studying
the emerging roles of lysosomes and for probing
the metabolic state of the lysosome in the various
diseases in which it is implicated.
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We thank all members of the Sabatini laboratory for helpful
insights, particularly J. R. Cantor, W. W. Chen, and J. M. Orozco;
C.A. Lewis and T. Kunchok from the Whitehead Institute
Metabolite Profiling Core Facility; and N. S. Gray (Dana-Farber
Cancer Institute) for Torin1. This work was supported by
grants from NIH (R01 CA103866, R01 CA129105, and R37
AI47389) and Department of Defense (W81XWH-15-1-0230) to
D.M.S., from Department of Defense (W81XWH-15-1-0337)
to E.F., and from the European Molecular Biology Organization
Long-Term Fellowship to M.A.-R.; a Saudi Aramco Ibn Khaldun
Fellowship for Saudi Women to N.N.L.; and fellowship support from
the National Defense Science and Engineering Graduate Fellowship
(NDSEG) Program to G.A. W. D.M.S. is an investigator of the
Howard Hughes Medical Institute.
Materials and Methods
Figs. S1 to S5
Tables S1 to S5
11 May 2017; accepted 3 October 2017
Published online 26 October 2017
SAMTOR is an S-adenosylmethionine
sensor for the mTORC1 pathway
Xin Gu,1,2,3,4 Jose M. Orozco,1,2,3,4 Robert A. Saxton,1,2,3,4 Kendall J. Condon,1,2,3,4
Grace Y. Liu,1,2,3,4 Patrycja A. Krawczyk,1,2,3,4 Sonia M. Scaria,1,2,3,4 J. Wade Harper,5
Steven P. Gygi,5 David M. Sabatini1,2,3,4†
m TOR complex 1 (m TORC1) regulates cell growth and metabolism in response to
multiple environmental cues. Nutrients signal via the Rag guanosine triphosphatases
(GTPases) to promote the localization of mTORC1 to the lysosomal surface, its site
of activation. We identified SAMTOR, a previously uncharacterized protein, which
inhibits m TORC1 signaling by interacting with GATOR1, the GTPase activating protein
(GAP) for RagA/B. We found that the methyl donor S-adenosylmethionine (SAM)
disrupts the SAMTOR-GATOR1 complex by binding directly to SAMTOR with a
dissociation constant of approximately 7 mM. In cells, methionine starvation reduces
SAM levels below this dissociation constant and promotes the association of SAMTOR
with GATOR1, thereby inhibiting m TORC1 signaling in a SAMTOR-dependent fashion.
Methionine-induced activation of mTORC1 requires the SAM binding capacity of SAMTOR.
Thus, SAMTOR is a SAM sensor that links methionine and one-carbon metabolism to
m TORC1 signaling.
The mechanistic target of rapamycin com- plex 1 (m TORC1) protein kinase is the cen- tral component of a pathway that regulates anabolic and catabolic processes in response to environmental signals, including growth
factors and nutrients (1–3). Amino acids promote
the translocation of mTORC1 to the lysosomal
surface, where its activator Rheb resides. This
localization depends on the heterodimeric Rag
GTPases, which consist of RagA or RagB bound
to RagC or RagD (4, 5).
The amino acid sensing pathway upstream
of m TORC1 is complicated, with several multi-
component complexes regulating the Rag hetero-
dimer, each likely conveying a distinct amino acid
input. GATOR1 and FLCN-FNIP are GAPs for
RagA/B and RagC/D, respectively (6, 7), whereas
Ragulator tethers the Rags to the lysosomal sur-
face and also has nucleotide exchange activity
(8, 9). The KICSTOR complex binds GATOR1 and
recruits it to the lysosome, and, like GATOR1, is
necessary for amino acid starvation to inhibit
m TORC1 signaling (7, 10, 11). The molecular func-
tion of GATOR2 is unknown, but it is required
for pathway activity and might act upstream of
Leucine and arginine are well-established
activators of m TORC1 signaling, and recent work
has shed light on the molecular mechanisms involved. The lysosomal transmembrane protein
SLC38A9 interacts with Ragulator (12–14) and is
a lysosomal arginine sensor (15), whereas Sestrin2
and CAS TOR1 are cytosolic leucine and arginine
sensors, respectively, that bind to and inhibit
the function of GATOR2 in the absence of their
cognate amino acids (16–19). Whether, and how,
other amino acids affect mTORC1 signaling is
To search for proteins that bind to GATOR1 or
KICSTOR, we mined the BioPlex protein-protein
interaction database generated by immunoprecipitation followed by mass spectrometry
1Whitehead Institute for Biomedical Research and Department
of Biology, Massachusetts Institute of Technology, Cambridge,
MA 02142, USA. 2Howard Hughes Medical Institute,
Department of Biology, Massachusetts Institute of Technology,
Cambridge, MA 02139, USA. 3Koch Institute for Integrative
Cancer Research and Department of Biology, Massachusetts
Institute of Technology, Cambridge, MA 02139, USA. 4Broad
Institute of Harvard and MIT, Cambridge, MA 02142, USA.
5Department of Cell Biology, Harvard Medical School, Boston,
MA 02115, USA.
*These authors contributed equally to this work.
†Corresponding author. Email: email@example.com