Inhibition of the Lysosomal Amino Acid Sensor SLC38A9 by the Membrane Microprotein SPAR

Gonen, T.; Saeher, A.; Mu, X.

doi:10.64898/2026.08.07.743590

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bioRxiv · 10.64898/2026.08.07.743590

Inhibition of the Lysosomal Amino Acid Sensor SLC38A9 by the Membrane Microprotein SPAR

Gonen, T.·Saeher, A.·Mu, X.

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Abstract

Long noncoding RNAs encode for microproteins that regulate cellular functions. Small regulatory peptide of amino acid response (SPAR) is a microprotein in the lysosome that responds to amino acid availability of the cell. In this study, we investigated the interactions between SPAR and SLC38A9, a lysosomal amino acid transporter and receptor involved in the mechanistic target of rapamycin 1 (mTORC1) pathway. We found that SPAR binds SLC38A9 and inhibits arginine transport in SLC38A9. Moreover, the downstream recruitment of Rag GTPases is also inhibited when SPAR is present in SLC38A9 liposomes. Docking model shows potential interactions between SPAR and SLC38A9. Together, these findings reveal the mechanism of mTORC1 inhibition through microprotein SPAR and illustrates the power of non long coding RNAs in altering cellular functions. Statement of SignificanceMicroproteins encoded from long noncoding RNAs are emerging as critical regulators of many pathways. This study investigates a novel mechanism of SPAR microprotein that directly regulates the mechanistic target of rapamycin complex1 (mTORC1) signaling pathway through the lysosomal amino acid transporter SLC38A9. SPAR blocks both arginine transport and the downstream recruitment of Rag GTPases. These findings provide critical results in how SPAR controls cellular amino acid availability, while broadly highlighting the powerful regulatory mechanism of microproteins in cellular processes.

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Gonen, T., Saeher, A., Mu, X.. 2026-08-10. Inhibition of the Lysosomal Amino Acid Sensor SLC38A9 by the Membrane Microprotein SPAR. https://doi.org/10.64898/2026.08.07.743590

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