The amino acid transporter SLC38A9 regulates MTORC1 and autophagy

Abstract

The mechanistic target of rapamycin (serine/threonine kinase) complex 1 (MTORC1) is a master regulator of macroautophagy (hereafter autophagy) that responds to different environmental nutrients, including amino acids, glucose, and growth factors. The identity of the amino acid-sensing component of the MTORC1 machinery had remained elusive until a lysosomal low-affinity amino acid transporter, SLC38A9 (solute carrier family 38, member 9), was recently characterized as a novel component of the Ragulator-RRAG GTPase complex by 3 independent research groups.

Keywords:

• autophagy
• lysosome
• RRAG GTPase
• stress
• TOR

By combining mass spectrometry analysis and co-immunoprecipitation, Rebsamen et al.,¹ Wang et al.² and Jung et al.³ identified interactions between SLC38A9 and several members of the Ragulator-LAMTOR complex and RRAG GTPases. The predicted cytoplasmic amino-terminal region of SLC38A9 is sufficient and required for the protein to bind the Ragulator-RRAG GTPase complex; however, the amino acid sensitive nature of the interaction between SLC38A9 and the RRAG GTPases is dependent on the transmembrane region of SLC38A9. Silencing of SLC38A9 represses MTORC1 activation by amino acids, and cells overexpressing SLC38A9 or its N-terminal region show prolonged MTORC1 activity upon amino acid starvation. These results indicate that SLC38A9 is an upstream amino acid-sensing activator of MTORC1.

The presence of amino acids switches the nucleotide loading status of RRAGA/RRAGB-RRAGC GTPase heterodimers, and nucleotide-loading is critical for the Ragulator-RRAG GTPase complex to bind MTOR. Therefore, the authors tested whether SLC38A9 interacts with the RRAG GTPases in a nucleotide loading status-dependent manner. Rebsamen et al. used different combinations of RRAGA, RRAGB or RRAGC mutants, which lock their nucleotide loading status, and showed that the RRAG GTPase heterodimers containing the low affinity/GDP-bound RRAGA^T21N or RRAGB^T54N interact with SLC38A9 better than the wild-type heterodimers. Conversely, the heterodimers containing the GTP-bound RRAGA^Q66L or RRAGB^Q99L, or the low affinity/GDP-bound RRAGC^S75N mutant partially or completely lose their interaction with SLC38A9. Wang et al.² and Jung et al.³ also show results consistent with these findings using nucleotide-binding mutants of the RRAG GTPases.

The authors also studied how SLC38A9 regulates autophagy, an important catabolic process inhibited by the MTORC1 pathway. Rebsamen et al. reported a delayed autophagy induction upon amino acid starvation in the cells stably expressing SLC38A9 based on the quantification of EGFP-LC3B labeled autophagosomes. Moreover, by overexpressing SLC38A9, they observed prolonged phosphorylation of a core component of the autophagy machinery, ULK1, which impaired autophagy, as well as sustained phosphorylation and decreased nuclear localization of the transcription factor TFEB, a master transcriptional activator of autophagy. Wang et al.² similarly found a suppression of autophagy induced by amino acid starvation in SLC38A9-overexpressing cells by detecting LC3B protein levels, whereas Jung et al.³ observed the same effect by monitoring changes in phosphorylation of ULK1.

These studies identified SLC38A9 as the first member of the amino acid sensing MTORC1 machinery that is capable of binding and transporting amino acids. SLC38A9 activates MTOR through its physical interaction with the Ragulator-RRAG GTPase complex when amino acids are present, and the overexpression of SLC38A9 results in sustained MTOR activation and a delayed autophagy induction upon amino acid starvation. Besides finding a missing piece of the MTORC1 signaling pathway, these studies also revealed SLC38A9 as a new potential therapeutic target for MTORC1 signaling- and autophagy-related diseases.

Funding

This work was supported by NIH grant GM053396 (to DJK) and a Rackham predoctoral fellowship (to MJ).