Alternative titles; symbols
HGNC Approved Gene Symbol: SLC38A9
Cytogenetic location: 5q11.2 Genomic coordinates (GRCh38): 5:55,625,845-55,712,335 (from NCBI)
SLC38A9, an amino acid transporter, is a constituent of a large lysosomal protein complex that senses and responds to amino acids (Rebsamen et al., 2015).
By searching databases for genes encoding SLC38 family members, Sundberg et al. (2008) identified SLC38A9. Quantitative real-time PCR detected weak Slc38a9 expression in all rat tissues examined. Highest expression was detected in testis and kidney.
In a review, Schioth et al. (2013) reported that the predicted SLC38A9 protein has 11 transmembrane domains, an intracellular N terminus, and an extracellular C terminus. SLC38A9 lacks an asparagine in transmembrane domain-1 that is conserved in all other SLC38 family members. Database analysis detected orthologs of SLC38A9 in multicellular organisms.
By immunohistochemical analysis of HeLa cells, Rebsamen et al. (2015) found that SLC38A9 colocalized with markers of late endosomes and lysosomes.
Wang et al. (2015) reported that 3 isoforms of SLC38A9 differ only in the length of the N-terminal domain, with the full-length, 561-amino acid isoform having a 119-amino acid N-terminal domain. All 3 isoforms have 11 transmembrane domains and 3 N-glycosylation sites in a luminal loop between transmembrane domains 3 and 4. All 3 isoforms localized to lysosomes.
Using tandem affinity purification, chromatography, and mass spectrometric analysis, Rebsamen et al. (2015) found that epitope-tagged SLC38A9 copurified with all 5 members of the Ragulator/LAMTOR (see LAMTOR1, 613510) complex and all 4 RAG GTPases (see RAGA, 612194) in transfected HEK293 cells. The complex also contained RAPTOR (RPTOR; 607130), which is involved in nutrient signaling by mTOR (601231) complex-1 (mTORC1). Coimmunoprecipitation analysis revealed specific recruitment of endogenous RAGA and LAMTOR1 with endogenous SLC38A9. Mutation analysis revealed that the N-terminal domain of SLC38A9, which is unique among SLC38 family members, was sufficient to bind Ragulator-RAG GTPases. When reconstituted in proteoliposomes, SLC38A9 transported radiolabeled glutamine. Transport required intraliposomal sodium and had a pH optimum of 5.5 to 6.5. SLC38A9 also transported radiolabeled arginine and asparagine, but not leucine or histidine. Kinetic analysis suggested that SLC38A9 may be a low-capacity transporter. Binding of SLC38A9 to RAG GTPases was influenced by nucleotide binding by the GTPase, suggesting conformation specificity. In transfected cells, amino acid starvation strengthened the interaction of epitope-tagged SLC38A9 with endogenous RAGC (RRAGC; 608267) and, to a minor extent, RAGA, but not with LAMTOR1 or LAMTOR3 (603296). In contrast to control cells that rapidly inactivated mTORC1 upon amino acid starvation, cells overexpressing SLC38A9 showed sustained mTORC1 activation upon amino acid starvation. Silencing of SLC38A9 in HEK293 or HeLa cells via short hairpin RNA dampened amino acid-induced mTORC1 activation. Rebsamen et al. (2015) concluded that SLC38A9 is an integral component of the lysosomal machinery that controls mTORC1 activity in response to amino acids.
Independently, Wang et al. (2015) identified the full-length SLC38A9 isoform as a critical component of the lysosomal Ragulator-RAG GTPase complex. SLC38A9 also coimmunoprecipitated with endogenous components of the v-ATPase (see 607027). SLC38A9 showed highest affinity for arginine when reconstituted into liposomes, and loss of SLC38A9 repressed mTORC1 activation by amino acids, particularly arginine. The N-terminal domain of SLC38A9 readily bound Ragulator and RAGs, but the interaction was insensitive to amino acids. Overexpression of full-length SLC38A9 in HEK293 cells rendered mTORC1 signaling resistant to amino acid starvation and suppressed mTORC1-induced autophagy with amino acid starvation. Overexpression of SLC38A9 isoforms with shorter N-terminal domains failed to maintain mTORC1 signaling following amino acid withdrawal. SLC38A9 also interacted with RAGB (RRAGB; 300725) heterodimers in the GDP-loaded state, but not in the GTP-bound state. Wang et al. (2015) concluded that SLC38A9 functions as an amino acid sensor for the mTORC1 pathway.
Rebsamen et al. (2015) identified SLC38A9 as a lysosomal membrane-resident protein competent in amino acid transport. Extensive functional proteomic analysis established SLC38A9 as an integral part of the Ragulator-RAG GTPases machinery. Gain of SLC38A9 function rendered cells resistant to amino acid withdrawal, whereas loss of SLC38A9 expression impaired amino acid-induced mTORC1 activation. Rebsamen et al. (2015) thus concluded that SLC38A9 is a physical and functional component of the amino acid-sensing machinery that controls the activation of mTOR.
Castellano et al. (2017) identified cholesterol, an essential building block for cellular growth, as a nutrient input that drives mTOR complex 1 (mTORC1; see 601231) recruitment and activation at the lysosomal surface. The lysosomal transmembrane protein SLC38A9 is required for mTORC1 activation by cholesterol through conserved cholesterol-responsive motifs. Moreover, SLC38A9 enables mTORC1 activation by cholesterol independently from its arginine-sensing function. Conversely, the Niemann-Pick C1 protein (NPC1; 607623), which regulates cholesterol export from the lysosome, binds to SLC38A9 and inhibits mTORC1 signaling through its sterol transport function. Castellano et al. (2017) concluded that, thus, lysosomal cholesterol drives mTORC1 activation and growth signaling through the SLC38A9-NPC1 complex.
Schioth et al. (2013) stated that the SLC38A9 gene maps to chromosome 5q11.2.
In their review, Schioth et al. (2013) reported that phylogenetic analysis suggested that SLC38A9 appeared late in evolution. In contrast, other SLC38 family members, such as SLC38A7 (614236), were present before the split of animals and plants.
Castellano, B. M., Thelen, A. M., Moldavski, O., Feltes, M., van der Welle, R. E. N., Mydock-McGrane, L., Jiang, X., van Eijkeren, R. J., Davis, O. B., Louie, S. M., Perera, R. M., Covey, D. F., Nomura, D. K., Ory, D. S., Zoncu, R. Lysosomal cholesterol activates mTORC1 via an SLC38A9-Niemann-Pick C1 signaling complex. Science 355: 1306-1311, 2017. [PubMed: 28336668] [Full Text: https://doi.org/10.1126/science.aag1417]
Rebsamen, M., Pochini, L., Stasyk, T., de Araujo, M. E. G., Galluccio, M., Kandasamy, R. K., Snijder, B., Fauster, A., Rudashevskaya, E. L., Bruckner, M., Scorzoni, S., Filipek, P. A., Huber, K. V. M., Bigenzahn, J. W., Heinz, L. X., Kraft, C., Bennett, K. L., Indiveri, C., Huber, L. A., Superti-Furga, G. SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature 519: 477-481, 2015. [PubMed: 25561175] [Full Text: https://doi.org/10.1038/nature14107]
Schioth, H. B., Roshanbin, S., Hagglund, M. G. A., Fredriksson, R. Evolutionary origin of amino acid transporter families SLC32, SL36 and SLC38 and physiological, pathological and therapeutic aspects. Molec. Aspects Med. 34: 571-585, 2013. [PubMed: 23506890] [Full Text: https://doi.org/10.1016/j.mam.2012.07.012]
Sundberg, B. E., Waag, E., Jacobsson, J. A., Stephansson, O., Rumaks, J., Svirskis, S., Alsio, J., Roman, E., Ebendal, T., Klusa, V., Fredriksson, R. The evolutionary history and tissue mapping of amino acid transporters belonging to solute carrier families SLC32, SLC36, and SLC38. J. Molec. Neurosci. 35: 179-193, 2008. [PubMed: 18418736] [Full Text: https://doi.org/10.1007/s12031-008-9046-x]
Wang, S., Tsun, Z.-Y., Wolfson, R. L., Shen, K., Wyant, G. A., Plovanich, M. E., Yuan, E. D., Jones, T. D., Chantranupong, L., Comb, W., Wang, T., Bar-Peled, L., Zoncu, R., Straub, C., Kim, C., Park, J., Sabatini, B. L., Sabatini, D. M. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science 347: 188-194, 2015. [PubMed: 25567906] [Full Text: https://doi.org/10.1126/science.1257132]