{"gene":"SLC38A9","run_date":"2026-06-10T07:46:33","timeline":{"discoveries":[{"year":2015,"finding":"SLC38A9 is a lysosomal transmembrane protein that physically interacts with the Rag GTPases and Ragulator complex in an amino acid-sensitive fashion, transports arginine with a high Km, and its loss represses mTORC1 activation by amino acids (particularly arginine); overexpression of SLC38A9 or just its Ragulator-binding domain makes mTORC1 signaling insensitive to amino acid starvation but not to Rag activity, placing SLC38A9 upstream of the Rag GTPases.","method":"Co-immunoprecipitation, amino acid transport assays, loss-of-function (knockdown/knockout) with mTORC1 activity readout, domain overexpression epistasis","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, transport assay, epistasis, replicated independently by multiple labs simultaneously","pmids":["25567906"],"is_preprint":false},{"year":2015,"finding":"SLC38A9 is an integral component of the Ragulator–RAG GTPase machinery at the lysosomal membrane; gain-of-function renders cells resistant to amino acid withdrawal and loss impairs amino-acid-induced mTORC1 activation, established by extensive functional proteomics and functional validation.","method":"Functional proteomics (AP-MS), gain/loss-of-function with mTORC1 activity readout, lysosomal fractionation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interactome mass spectrometry, gain/loss-of-function, independently replicated across labs","pmids":["25561175"],"is_preprint":false},{"year":2015,"finding":"SLC38A9 is an 11-pass lysosomal transmembrane protein that associates with Rag GTPases in an amino acid-sensitive and nucleotide binding state-dependent manner; SLC38A9 depletion inhibits mTORC1 activity in the presence of amino acids; overexpression causes RHEB-dependent hyperactivation of mTORC1; during amino acid starvation, mTOR is retained at the lysosome upon SLC38A9 depletion but fails to be activated.","method":"Co-immunoprecipitation, siRNA knockdown/overexpression with mTORC1 readout, lysosomal localization by fluorescence microscopy","journal":"Molecular and Cellular Biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, localization, epistasis with RHEB), independently corroborates two simultaneous publications","pmids":["25963655"],"is_preprint":false},{"year":2017,"finding":"SLC38A9 mediates the transport of many essential amino acids (including leucine) out of lysosomes in an arginine-regulated fashion; it is required for leucine generated via lysosomal proteolysis to exit lysosomes and activate mTORC1; pancreatic cancer cells using macropinocytosed protein as a nutrient source require SLC38A9 to form tumors.","method":"Isotope tracing/transport assays, lysosome immunopurification (Lyso-IP), SLC38A9 knockout cells, tumor formation assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro transport reconstitution with isotope tracing, lysosome purification, KO with multiple functional readouts","pmids":["29053970"],"is_preprint":false},{"year":2017,"finding":"Lysosomal cholesterol activates mTORC1 through SLC38A9 via conserved cholesterol-responsive motifs; SLC38A9 enables mTORC1 activation by cholesterol independently from its arginine-sensing function; NPC1 binds to SLC38A9 and inhibits mTORC1 signaling through its sterol transport function.","method":"Co-immunoprecipitation (SLC38A9–NPC1 interaction), cholesterol depletion/repletion experiments, mutagenesis of cholesterol-responsive motifs, loss-of-function with mTORC1 readout","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of responsive motifs, loss-of-function, published in high-impact journal with multiple orthogonal methods","pmids":["28336668"],"is_preprint":false},{"year":2018,"finding":"Ragulator and SLC38A9 are each guanine nucleotide exchange factors (GEFs) that collectively push Rag GTPases toward the active state: Ragulator triggers GTP release from RagC (resolving the locked inactive state), while upon arginine binding, SLC38A9 converts RagA from GDP- to GTP-loaded state, activating the Rag GTPase heterodimer.","method":"GEF activity assay (nucleotide exchange biochemistry), reconstituted Rag GTPase assays, arginine-binding experiments","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro GEF activity reconstitution with defined substrates, mechanistic dissection of RagA vs RagC specificity, single lab","pmids":["30181260"],"is_preprint":false},{"year":2018,"finding":"Crystal structure of zebrafish SLC38A9 in complex with arginine captured in the cytosol-open state; the bound arginine is locked in a transitional state stabilized by TM1 anchored at the groove between TM5 and TM7 via the conserved WNTMM motif; mutations in the WNTMM motif abolish arginine transport.","method":"X-ray crystallography, site-directed mutagenesis, arginine transport assay","journal":"Nature Structural & Molecular Biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional mutagenesis validation in single rigorous study","pmids":["29872228"],"is_preprint":false},{"year":2019,"finding":"Human SLC38A9 reconstituted in liposomes transports both glutamine and arginine with cooperative kinetics; a Na+ binding site at T453 was identified by mutagenesis; cholesterol stimulates glutamine and arginine transport; the N-terminal tail is not required for intrinsic transport function; SLC38A9 is competent for glutamine efflux but arginine efflux is negligible; arginine acts as a modulator stimulating glutamine efflux; glutamine and arginine likely bind to different sites.","method":"Protein reconstitution in liposomes, transport assays, site-directed mutagenesis, bioinformatics-guided mutagenesis, N-terminal deletion mutant","journal":"Biochimica et Biophysica Acta – Biomembranes","confidence":"High","confidence_rationale":"Tier 1 / Moderate — full reconstitution with transport assay and mutagenesis, multiple orthogonal approaches, single lab","pmids":["31295473"],"is_preprint":false},{"year":2020,"finding":"The cytoplasmic tail of SLC38A9 destabilizes the lysosomal folliculin complex (LFC, consisting of inactive Rag dimer, Ragulator, and FLCN:FNIP2 GAP), triggering GAP activity of FLCN:FNIP2 toward RagC; cryo-EM structures of Rags–Ragulator–SLC38A9 cytoplasmic tail in pre- and post-GTP hydrolysis states of RagC explain mechanistically how SLC38A9 promotes Rag dimer activation.","method":"Cryo-EM structure determination, in vitro GAP activity assay, biochemical reconstitution of LFC disassembly","journal":"Nature Structural & Molecular Biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structures at two functional states combined with in vitro GAP activity assay, single lab with multiple orthogonal methods","pmids":["32868926"],"is_preprint":false},{"year":2021,"finding":"SLC38A9 interacts with SLC36A1 in C2C12 cells; they enhance each other's expression levels and lysosomal surface localization; SLC38A9 interacting proteins in C2C12 cells participate in amino acid sensing, mTORC1 signaling, and protein synthesis pathways.","method":"Co-immunoprecipitation, immunofluorescence co-localization, proteomics of SLC38A9 interactors","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single Co-IP and co-localization, single lab, limited mechanistic follow-up","pmids":["34572527"],"is_preprint":false},{"year":2021,"finding":"ATF4 binds to two amino acid response elements (AAREs) found in the SLC38A9 promoter/first intron region and regulates SLC38A9 mRNA expression in porcine skeletal muscle cells; the AARE in the first intron is located in the core promoter region of SLC38A9.","method":"Promoter analysis, chromatin immunoprecipitation / AARE binding assay, siRNA knockdown of ATF4, RT-qPCR","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct binding assay with ATF4 and AARE, single lab, single organism (porcine)","pmids":["34246831"],"is_preprint":false},{"year":2024,"finding":"SLC38A9 interacts with the SARS-CoV-2 S1 protein multibasic motif in the endolysosome; SLC38A9 knockdown prevents S1-induced endolysosome de-acidification and blocks S protein-mediated entry of pseudo-SARS-CoV-2 in multiple cell lines.","method":"Co-immunoprecipitation (SLC38A9–S1 interaction), siRNA knockdown, pseudo-virus entry assay, endolysosomal pH measurement","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP of interaction plus functional KD with viral entry readout, single lab","pmids":["39071889"],"is_preprint":false},{"year":2025,"finding":"HIV-1 Tat interacts with SLC38A9 via its arginine-rich basic domain in the endolysosome; this interaction leads to endolysosome dysfunction, enhanced HIV-1 LTR transactivation, and cellular senescence in human astrocytes.","method":"Co-immunoprecipitation, domain mapping (arginine-rich domain), endolysosomal function assays, senescence assays","journal":"Life Science Alliance","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP with domain mapping and functional readouts, single lab","pmids":["40324823"],"is_preprint":false},{"year":2023,"finding":"RBM25 binds to and regulates alternative splicing of Slc38a9 in H9c2 cardiomyocyte cells, as established by iRIP-seq binding identification and RT-qPCR validation.","method":"iRIP-seq, RNA-seq, RT-qPCR validation","journal":"PeerJ","confidence":"Low","confidence_rationale":"Tier 3 / Weak — binding identified by iRIP-seq confirmed by RT-qPCR, no functional consequence of SLC38A9 splicing change demonstrated","pmids":["37953772"],"is_preprint":false},{"year":2024,"finding":"SLC38A9 promotes outward lysosome transport along a SLC38A9-BORC-kinesin 1/3 axis in response to amino acids; this lysosome dispersal function is distinct from its mTORC1-activating arginine-sensing function; aromatic amino acids (e.g., phenylalanine) promote lysosome peripheral redistribution via SLC38A9, and combining lysosome-dispersing amino acids with arginine synergistically enhances mTOR activation in a kinesin 1/3-dependent manner.","method":"High-content imaging of lysosome positioning, kinesin 1/3 KO cells, SLC38A9 perturbation, amino acid titrations with mTOR readout","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, imaging-based functional assay with KO, single lab, mechanistic details of SLC38A9 in BORC axis not fully biochemically validated","pmids":["bio_10.1101_2024.10.12.618047"],"is_preprint":true},{"year":2025,"finding":"Arginine uptake by SLC38A9 is pH-dependent; His544 serves as the pH sensor, with its protonation/deprotonation influencing transport; mutating His544 abolishes pH dependence of arginine uptake without impairing overall transport activity, indicating His544 is not directly involved in substrate binding; two SLC38A9 structures at high and low pH reveal the structural basis of pH-induced activation.","method":"Transport assays at different pH, site-directed mutagenesis of His544, cryo-EM/structural comparison at two pH values","journal":"FEBS Letters / bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro transport assay with mutagenesis and structural comparison, single lab, peer-reviewed publication","pmids":["42070976","41279478"],"is_preprint":false}],"current_model":"SLC38A9 is a lysosomal 11-pass transmembrane transporter and arginine sensor that physically associates with the Ragulator–Rag GTPase complex; upon arginine binding, it acts as a GEF to load RagA with GTP and destabilizes the inhibitory folliculin complex (LFC) to release FLCN:FNIP2 GAP activity toward RagC, collectively driving the Rag GTPases into their active state and recruiting mTORC1 to the lysosomal surface; it also mediates arginine-regulated efflux of essential amino acids (including leucine) from lysosomes to sustain cytosolic mTORC1 activation, senses lysosomal cholesterol through conserved motifs in a complex with NPC1, and its transport activity is further regulated by lysosomal pH through the His544 residue."},"narrative":{"mechanistic_narrative":"SLC38A9 is a multi-pass lysosomal transmembrane transporter that serves as an amino acid sensor coupling lysosomal nutrient content to mTORC1 activation [PMID:25567906, PMID:25561175]. It physically associates with the Rag GTPase–Ragulator machinery at the lysosomal membrane in an amino-acid-sensitive, nucleotide-state-dependent manner, and acts upstream of the Rag GTPases: its loss blocks amino-acid (especially arginine)-induced mTORC1 activation, while overexpression renders mTORC1 signaling resistant to amino acid withdrawal [PMID:25567906, PMID:25561175, PMID:25963655]. Mechanistically, arginine binding converts SLC38A9 into a guanine nucleotide exchange factor that loads RagA with GTP, and its cytoplasmic tail destabilizes the inhibitory folliculin complex to release FLCN:FNIP2 GAP activity toward RagC, together driving the Rag heterodimer to its active conformation [PMID:30181260, PMID:32868926]. Beyond sensing, SLC38A9 functions as a transporter that effluxes essential amino acids including leucine from lysosomes in an arginine-regulated fashion, enabling leucine generated by lysosomal proteolysis to exit and sustain mTORC1; this efflux activity is required for pancreatic cancer cells to use macropinocytosed protein for tumor growth [PMID:29053970]. Structural studies of the arginine-bound transporter define a conserved WNTMM motif essential for arginine transport [PMID:29872228], and reconstitution shows cooperative glutamine and arginine transport with a Na+ site at T453, cholesterol-stimulated activity, and arginine acting as a modulator of glutamine efflux [PMID:31295473]. SLC38A9 additionally links lysosomal cholesterol to mTORC1 through conserved cholesterol-responsive motifs and a complex with NPC1, independently of its arginine-sensing function [PMID:28336668]. Its arginine transport is further gated by lysosomal pH via the protonation state of His544 [PMID:42070976, PMID:41279478].","teleology":[{"year":2015,"claim":"Established the identity of the lysosomal amino acid sensor feeding mTORC1: before this, how amino acids signaled to the Rag GTPases at the lysosome was unknown.","evidence":"Reciprocal Co-IP, amino acid transport assays, and loss/gain-of-function epistasis with mTORC1 readouts placing SLC38A9 upstream of the Rags, replicated across labs","pmids":["25567906","25561175","25963655"],"confidence":"High","gaps":["Did not resolve the biochemical mechanism by which SLC38A9 activates the Rag GTPases","High Km arginine transport left the physiological transport substrate and direction unclear"]},{"year":2017,"claim":"Resolved what SLC38A9 actually transports physiologically, showing it effluxes essential amino acids including leucine from lysosomes to sustain mTORC1 and support nutrient scavenging.","evidence":"Isotope-tracing transport assays, lysosome immunopurification, and knockout cells with tumor-formation readouts in pancreatic cancer","pmids":["29053970"],"confidence":"High","gaps":["Did not separate transport-dependent from sensing-dependent contributions to mTORC1 in all contexts","Mechanism coupling efflux to Rag activation not structurally defined"]},{"year":2017,"claim":"Extended SLC38A9 sensing beyond amino acids by showing it conveys a lysosomal cholesterol signal to mTORC1 in complex with NPC1.","evidence":"Reciprocal Co-IP of SLC38A9–NPC1, mutagenesis of cholesterol-responsive motifs, and cholesterol depletion/repletion with mTORC1 readouts","pmids":["28336668"],"confidence":"High","gaps":["Structural basis of cholesterol recognition not determined","Relationship between cholesterol sensing and transport conformational cycle unresolved"]},{"year":2018,"claim":"Defined the biochemical activity behind Rag activation, showing SLC38A9 is an arginine-stimulated GEF that loads RagA with GTP.","evidence":"In vitro nucleotide-exchange GEF assays with reconstituted Rag GTPases and arginine-binding experiments","pmids":["30181260"],"confidence":"High","gaps":["Did not provide structural snapshots of the SLC38A9–Rag intermediate","GEF activity toward RagA vs Ragulator GEF toward RagC integration not fully reconstituted"]},{"year":2018,"claim":"Provided the atomic basis of arginine recognition by the transporter, identifying the WNTMM motif required for transport.","evidence":"X-ray crystal structure of zebrafish SLC38A9 in cytosol-open state bound to arginine with site-directed mutagenesis and transport assays","pmids":["29872228"],"confidence":"High","gaps":["Single conformational state captured; full transport cycle not visualized","Human protein structure not solved in this work"]},{"year":2019,"claim":"Reconstituted the human transporter to define substrate kinetics, ion coupling, and the distinct roles of arginine and glutamine.","evidence":"Proteoliposome transport assays, mutagenesis identifying a Na+ site at T453, and N-terminal deletion analysis","pmids":["31295473"],"confidence":"High","gaps":["Physiological relevance of glutamine efflux vs arginine modulation in cells not established","Two-site binding model for glutamine and arginine inferred but not structurally confirmed"]},{"year":2020,"claim":"Explained mechanistically how the cytoplasmic tail activates Rags by destabilizing the inhibitory folliculin complex to trigger FLCN:FNIP2 GAP activity toward RagC.","evidence":"Cryo-EM structures of Rags–Ragulator–SLC38A9 tail in pre- and post-GTP-hydrolysis states with in vitro GAP assays","pmids":["32868926"],"confidence":"High","gaps":["How arginine occupancy of the transmembrane domain is communicated to the cytoplasmic tail not resolved","Single-lab structural model"]},{"year":2021,"claim":"Mapped additional lysosomal interaction partners and transcriptional control, linking SLC38A9 to SLC36A1 and to ATF4-driven amino acid response regulation.","evidence":"Co-IP and co-localization with SLC36A1 in C2C12 cells; promoter/AARE binding analysis and ATF4 knockdown in porcine muscle cells","pmids":["34572527","34246831"],"confidence":"Medium","gaps":["Functional consequence of SLC36A1–SLC38A9 mutual stabilization not mechanistically dissected","ATF4 regulation shown in single species without conservation testing"]},{"year":2024,"claim":"Identified roles for SLC38A9 in viral entry and a transport-independent lysosome-positioning function, broadening its cellular involvement.","evidence":"Co-IP with SARS-CoV-2 S1 and HIV-1 Tat basic domains plus functional knockdown; high-content lysosome-positioning imaging along a BORC–kinesin axis (preprint)","pmids":["39071889","40324823","bio_10.1101_2024.10.12.618047"],"confidence":"Medium","gaps":["Lysosome-dispersal axis is preprint and not biochemically validated","Pathogen-protein interactions are single-lab with limited mechanistic depth"]},{"year":2025,"claim":"Showed lysosomal pH gates SLC38A9 transport through a defined histidine sensor, connecting organelle pH to nutrient sensing.","evidence":"Transport assays at varying pH, His544 mutagenesis, and structural comparison at high and low pH","pmids":["42070976","41279478"],"confidence":"Medium","gaps":["Physiological impact of pH gating on mTORC1 output not tested in cells","Single-lab structural and functional dataset"]},{"year":null,"claim":"How the transmembrane substrate-binding events (arginine, glutamine, cholesterol, pH) are integrated and conformationally transmitted to the cytoplasmic GEF/LFC-destabilizing tail to time Rag activation remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No full-length human structure coupling transport state to Rag-activation state","Quantitative contribution of transport vs sensing to mTORC1 in vivo not separated","Integration of cholesterol and pH signals with arginine sensing not mechanistically unified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,3,6,7]},{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[0,4,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,8]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,2,3]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2,5,8]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[3]},{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[3,7]}],"complexes":["Rag GTPase–Ragulator complex","lysosomal folliculin complex (LFC)"],"partners":["RAGA","RAGC","RAGULATOR","FLCN","FNIP2","NPC1","SLC36A1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NBW4","full_name":"Neutral amino acid transporter 9","aliases":["Solute carrier family 38 member 9","Up-regulated in lung cancer 11"],"length_aa":561,"mass_kda":63.8,"function":"Lysosomal amino acid transporter involved in the activation of mTORC1 in response to amino acid levels (PubMed:25561175, PubMed:25567906, PubMed:29053970). Probably acts as an amino acid sensor of the Rag GTPases and Ragulator complexes, 2 complexes involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids (PubMed:25567906, PubMed:29053970). Following activation by amino acids, the Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated (PubMed:25561175, PubMed:25567906). SLC38A9 mediates transport of amino acids with low capacity and specificity with a slight preference for polar amino acids (PubMed:25561175, PubMed:25567906). Acts as an arginine sensor (PubMed:25567906, PubMed:29053970, PubMed:31295473). Following activation by arginine binding, mediates transport of L-glutamine, leucine and tyrosine with high efficiency, and is required for the efficient utilization of these amino acids after lysosomal protein degradation (PubMed:29053970, PubMed:31295473). However, the transport mechanism is not well defined and the role of sodium is not clear (PubMed:25561175, PubMed:31295473). Can disassemble the lysosomal folliculin complex (LFC), and thereby triggers GAP activity of FLCN:FNIP2 toward RRAGC (PubMed:32868926). Acts as an cholesterol sensor that conveys increases in lysosomal cholesterol, leading to lysosomal recruitment and activation of mTORC1 via the Rag GTPases (PubMed:28336668). Guanine exchange factor (GEF) that, upon arginine binding, stimulates GDP release from RRAGA and therefore activates the Rag GTPase heterodimer and the mTORC1 pathway in response to nutrient sufficiency (PubMed:30181260)","subcellular_location":"Lysosome membrane; Late endosome membrane","url":"https://www.uniprot.org/uniprotkb/Q8NBW4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SLC38A9","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SLC38A9","total_profiled":1310},"omim":[{"mim_id":"616203","title":"SOLUTE CARRIER FAMILY 38, MEMBER 9; SLC38A9","url":"https://www.omim.org/entry/616203"},{"mim_id":"613510","title":"LATE ENDOSOMAL/LYSOSOMAL ADAPTOR, MAPK AND MTOR ACTIVATOR 1; LAMTOR1","url":"https://www.omim.org/entry/613510"},{"mim_id":"607623","title":"NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1; NPC1","url":"https://www.omim.org/entry/607623"},{"mim_id":"601231","title":"MECHANISTIC TARGET OF RAPAMYCIN; MTOR","url":"https://www.omim.org/entry/601231"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"placenta","ntpm":54.3}],"url":"https://www.proteinatlas.org/search/SLC38A9"},"hgnc":{"alias_symbol":["FLJ90709","SNAT9"],"prev_symbol":[]},"alphafold":{"accession":"Q8NBW4","domains":[{"cath_id":"-","chopping":"43-105","consensus_level":"high","plddt":59.7457,"start":43,"end":105},{"cath_id":"1.20.1740.10","chopping":"118-249_285-559","consensus_level":"medium","plddt":86.5171,"start":118,"end":559}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NBW4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NBW4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NBW4-F1-predicted_aligned_error_v6.png","plddt_mean":76.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SLC38A9","jax_strain_url":"https://www.jax.org/strain/search?query=SLC38A9"},"sequence":{"accession":"Q8NBW4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NBW4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NBW4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NBW4"}},"corpus_meta":[{"pmid":"25567906","id":"PMC_25567906","title":"Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1.","date":"2015","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/25567906","citation_count":686,"is_preprint":false},{"pmid":"25561175","id":"PMC_25561175","title":"SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1.","date":"2015","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/25561175","citation_count":557,"is_preprint":false},{"pmid":"28336668","id":"PMC_28336668","title":"Lysosomal cholesterol activates mTORC1 via an SLC38A9-Niemann-Pick C1 signaling complex.","date":"2017","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28336668","citation_count":445,"is_preprint":false},{"pmid":"29053970","id":"PMC_29053970","title":"mTORC1 Activator SLC38A9 Is Required to Efflux Essential Amino Acids from Lysosomes and Use Protein as a Nutrient.","date":"2017","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/29053970","citation_count":369,"is_preprint":false},{"pmid":"25963655","id":"PMC_25963655","title":"Amino Acid-Dependent mTORC1 Regulation by the Lysosomal Membrane Protein SLC38A9.","date":"2015","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25963655","citation_count":220,"is_preprint":false},{"pmid":"30181260","id":"PMC_30181260","title":"Ragulator and SLC38A9 activate the Rag GTPases through noncanonical GEF mechanisms.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30181260","citation_count":120,"is_preprint":false},{"pmid":"32868926","id":"PMC_32868926","title":"Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.","date":"2020","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/32868926","citation_count":53,"is_preprint":false},{"pmid":"29872228","id":"PMC_29872228","title":"Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state.","date":"2018","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29872228","citation_count":50,"is_preprint":false},{"pmid":"26431368","id":"PMC_26431368","title":"SLC38A9: A lysosomal amino acid transporter at the core of the amino acid-sensing machinery that controls MTORC1.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26431368","citation_count":29,"is_preprint":false},{"pmid":"31295473","id":"PMC_31295473","title":"Insights into the transport side of the human SLC38A9 transceptor.","date":"2019","source":"Biochimica et biophysica acta. Biomembranes","url":"https://pubmed.ncbi.nlm.nih.gov/31295473","citation_count":25,"is_preprint":false},{"pmid":"26506891","id":"PMC_26506891","title":"The amino acid transporter SLC38A9 regulates MTORC1 and autophagy.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26506891","citation_count":12,"is_preprint":false},{"pmid":"38638435","id":"PMC_38638435","title":"Arginine alleviates Clostridium perfringens α toxin-induced intestinal injury in vivo and in vitro via the SLC38A9/mTORC1 pathway.","date":"2024","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/38638435","citation_count":10,"is_preprint":false},{"pmid":"34572527","id":"PMC_34572527","title":"Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells.","date":"2021","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/34572527","citation_count":10,"is_preprint":false},{"pmid":"35457018","id":"PMC_35457018","title":"Slc38a9 Deficiency Induces Apoptosis and Metabolic Dysregulation and Leads to Premature Death in Zebrafish.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35457018","citation_count":8,"is_preprint":false},{"pmid":"40613244","id":"PMC_40613244","title":"mTORC1 Selective Nano-Inhibitor by Disrupting the Lysosomal Arginine-SLC38A9- mTORC1-CDKs Axis for Precision Bladder Cancer Therapy.","date":"2025","source":"Advanced materials (Deerfield Beach, Fla.)","url":"https://pubmed.ncbi.nlm.nih.gov/40613244","citation_count":7,"is_preprint":false},{"pmid":"34685533","id":"PMC_34685533","title":"Arginine Regulates TOR Signaling Pathway through SLC38A9 in Abalone Haliotis discus 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and Vascular Complications.","date":"2022","source":"Nutrients","url":"https://pubmed.ncbi.nlm.nih.gov/36364703","citation_count":2,"is_preprint":false},{"pmid":"40324823","id":"PMC_40324823","title":"SLC38A9 is directly involved in Tat-induced endolysosome dysfunction and senescence in astrocytes.","date":"2025","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/40324823","citation_count":1,"is_preprint":false},{"pmid":"41279478","id":"PMC_41279478","title":"pH-dependent regulation in SLC38A9.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41279478","citation_count":0,"is_preprint":false},{"pmid":"42186568","id":"PMC_42186568","title":"Lysosomal protein SLC38A9 regulates arginine-mediated autophagy, ER stress, and apoptosis in abalone Haliotis discus hannai.","date":"2026","source":"Marine life science & technology","url":"https://pubmed.ncbi.nlm.nih.gov/42186568","citation_count":0,"is_preprint":false},{"pmid":"42070976","id":"PMC_42070976","title":"pH-mediated activation of the lysosomal arginine sensor SLC38A9.","date":"2026","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/42070976","citation_count":0,"is_preprint":false},{"pmid":"41811103","id":"PMC_41811103","title":"SLC38A9 Regulation Affects Hippocampal Neuronal Autophagy: A Potential Alzheimer's Therapeutic Approach by Suppressing Alzheimer's Disease-Related Protein Deposition.","date":"2026","source":"CNS neuroscience & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/41811103","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.12.618047","title":"Synergistic Role of Amino Acids in Enhancing mTOR Activation Through Lysosome Positioning","date":"2024-10-13","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.12.618047","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14799,"output_tokens":4122,"usd":0.053114,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11842,"output_tokens":3721,"usd":0.076118,"stage2_stop_reason":"end_turn"},"total_usd":0.129232,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"SLC38A9 is a lysosomal transmembrane protein that physically interacts with the Rag GTPases and Ragulator complex in an amino acid-sensitive fashion, transports arginine with a high Km, and its loss represses mTORC1 activation by amino acids (particularly arginine); overexpression of SLC38A9 or just its Ragulator-binding domain makes mTORC1 signaling insensitive to amino acid starvation but not to Rag activity, placing SLC38A9 upstream of the Rag GTPases.\",\n      \"method\": \"Co-immunoprecipitation, amino acid transport assays, loss-of-function (knockdown/knockout) with mTORC1 activity readout, domain overexpression epistasis\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, transport assay, epistasis, replicated independently by multiple labs simultaneously\",\n      \"pmids\": [\"25567906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SLC38A9 is an integral component of the Ragulator–RAG GTPase machinery at the lysosomal membrane; gain-of-function renders cells resistant to amino acid withdrawal and loss impairs amino-acid-induced mTORC1 activation, established by extensive functional proteomics and functional validation.\",\n      \"method\": \"Functional proteomics (AP-MS), gain/loss-of-function with mTORC1 activity readout, lysosomal fractionation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interactome mass spectrometry, gain/loss-of-function, independently replicated across labs\",\n      \"pmids\": [\"25561175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SLC38A9 is an 11-pass lysosomal transmembrane protein that associates with Rag GTPases in an amino acid-sensitive and nucleotide binding state-dependent manner; SLC38A9 depletion inhibits mTORC1 activity in the presence of amino acids; overexpression causes RHEB-dependent hyperactivation of mTORC1; during amino acid starvation, mTOR is retained at the lysosome upon SLC38A9 depletion but fails to be activated.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown/overexpression with mTORC1 readout, lysosomal localization by fluorescence microscopy\",\n      \"journal\": \"Molecular and Cellular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, localization, epistasis with RHEB), independently corroborates two simultaneous publications\",\n      \"pmids\": [\"25963655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SLC38A9 mediates the transport of many essential amino acids (including leucine) out of lysosomes in an arginine-regulated fashion; it is required for leucine generated via lysosomal proteolysis to exit lysosomes and activate mTORC1; pancreatic cancer cells using macropinocytosed protein as a nutrient source require SLC38A9 to form tumors.\",\n      \"method\": \"Isotope tracing/transport assays, lysosome immunopurification (Lyso-IP), SLC38A9 knockout cells, tumor formation assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro transport reconstitution with isotope tracing, lysosome purification, KO with multiple functional readouts\",\n      \"pmids\": [\"29053970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Lysosomal cholesterol activates mTORC1 through SLC38A9 via conserved cholesterol-responsive motifs; SLC38A9 enables mTORC1 activation by cholesterol independently from its arginine-sensing function; NPC1 binds to SLC38A9 and inhibits mTORC1 signaling through its sterol transport function.\",\n      \"method\": \"Co-immunoprecipitation (SLC38A9–NPC1 interaction), cholesterol depletion/repletion experiments, mutagenesis of cholesterol-responsive motifs, loss-of-function with mTORC1 readout\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of responsive motifs, loss-of-function, published in high-impact journal with multiple orthogonal methods\",\n      \"pmids\": [\"28336668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Ragulator and SLC38A9 are each guanine nucleotide exchange factors (GEFs) that collectively push Rag GTPases toward the active state: Ragulator triggers GTP release from RagC (resolving the locked inactive state), while upon arginine binding, SLC38A9 converts RagA from GDP- to GTP-loaded state, activating the Rag GTPase heterodimer.\",\n      \"method\": \"GEF activity assay (nucleotide exchange biochemistry), reconstituted Rag GTPase assays, arginine-binding experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro GEF activity reconstitution with defined substrates, mechanistic dissection of RagA vs RagC specificity, single lab\",\n      \"pmids\": [\"30181260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Crystal structure of zebrafish SLC38A9 in complex with arginine captured in the cytosol-open state; the bound arginine is locked in a transitional state stabilized by TM1 anchored at the groove between TM5 and TM7 via the conserved WNTMM motif; mutations in the WNTMM motif abolish arginine transport.\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, arginine transport assay\",\n      \"journal\": \"Nature Structural & Molecular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional mutagenesis validation in single rigorous study\",\n      \"pmids\": [\"29872228\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Human SLC38A9 reconstituted in liposomes transports both glutamine and arginine with cooperative kinetics; a Na+ binding site at T453 was identified by mutagenesis; cholesterol stimulates glutamine and arginine transport; the N-terminal tail is not required for intrinsic transport function; SLC38A9 is competent for glutamine efflux but arginine efflux is negligible; arginine acts as a modulator stimulating glutamine efflux; glutamine and arginine likely bind to different sites.\",\n      \"method\": \"Protein reconstitution in liposomes, transport assays, site-directed mutagenesis, bioinformatics-guided mutagenesis, N-terminal deletion mutant\",\n      \"journal\": \"Biochimica et Biophysica Acta – Biomembranes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — full reconstitution with transport assay and mutagenesis, multiple orthogonal approaches, single lab\",\n      \"pmids\": [\"31295473\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The cytoplasmic tail of SLC38A9 destabilizes the lysosomal folliculin complex (LFC, consisting of inactive Rag dimer, Ragulator, and FLCN:FNIP2 GAP), triggering GAP activity of FLCN:FNIP2 toward RagC; cryo-EM structures of Rags–Ragulator–SLC38A9 cytoplasmic tail in pre- and post-GTP hydrolysis states of RagC explain mechanistically how SLC38A9 promotes Rag dimer activation.\",\n      \"method\": \"Cryo-EM structure determination, in vitro GAP activity assay, biochemical reconstitution of LFC disassembly\",\n      \"journal\": \"Nature Structural & Molecular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structures at two functional states combined with in vitro GAP activity assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"32868926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SLC38A9 interacts with SLC36A1 in C2C12 cells; they enhance each other's expression levels and lysosomal surface localization; SLC38A9 interacting proteins in C2C12 cells participate in amino acid sensing, mTORC1 signaling, and protein synthesis pathways.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence co-localization, proteomics of SLC38A9 interactors\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP and co-localization, single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"34572527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ATF4 binds to two amino acid response elements (AAREs) found in the SLC38A9 promoter/first intron region and regulates SLC38A9 mRNA expression in porcine skeletal muscle cells; the AARE in the first intron is located in the core promoter region of SLC38A9.\",\n      \"method\": \"Promoter analysis, chromatin immunoprecipitation / AARE binding assay, siRNA knockdown of ATF4, RT-qPCR\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct binding assay with ATF4 and AARE, single lab, single organism (porcine)\",\n      \"pmids\": [\"34246831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SLC38A9 interacts with the SARS-CoV-2 S1 protein multibasic motif in the endolysosome; SLC38A9 knockdown prevents S1-induced endolysosome de-acidification and blocks S protein-mediated entry of pseudo-SARS-CoV-2 in multiple cell lines.\",\n      \"method\": \"Co-immunoprecipitation (SLC38A9–S1 interaction), siRNA knockdown, pseudo-virus entry assay, endolysosomal pH measurement\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP of interaction plus functional KD with viral entry readout, single lab\",\n      \"pmids\": [\"39071889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HIV-1 Tat interacts with SLC38A9 via its arginine-rich basic domain in the endolysosome; this interaction leads to endolysosome dysfunction, enhanced HIV-1 LTR transactivation, and cellular senescence in human astrocytes.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping (arginine-rich domain), endolysosomal function assays, senescence assays\",\n      \"journal\": \"Life Science Alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP with domain mapping and functional readouts, single lab\",\n      \"pmids\": [\"40324823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RBM25 binds to and regulates alternative splicing of Slc38a9 in H9c2 cardiomyocyte cells, as established by iRIP-seq binding identification and RT-qPCR validation.\",\n      \"method\": \"iRIP-seq, RNA-seq, RT-qPCR validation\",\n      \"journal\": \"PeerJ\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — binding identified by iRIP-seq confirmed by RT-qPCR, no functional consequence of SLC38A9 splicing change demonstrated\",\n      \"pmids\": [\"37953772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SLC38A9 promotes outward lysosome transport along a SLC38A9-BORC-kinesin 1/3 axis in response to amino acids; this lysosome dispersal function is distinct from its mTORC1-activating arginine-sensing function; aromatic amino acids (e.g., phenylalanine) promote lysosome peripheral redistribution via SLC38A9, and combining lysosome-dispersing amino acids with arginine synergistically enhances mTOR activation in a kinesin 1/3-dependent manner.\",\n      \"method\": \"High-content imaging of lysosome positioning, kinesin 1/3 KO cells, SLC38A9 perturbation, amino acid titrations with mTOR readout\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, imaging-based functional assay with KO, single lab, mechanistic details of SLC38A9 in BORC axis not fully biochemically validated\",\n      \"pmids\": [\"bio_10.1101_2024.10.12.618047\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Arginine uptake by SLC38A9 is pH-dependent; His544 serves as the pH sensor, with its protonation/deprotonation influencing transport; mutating His544 abolishes pH dependence of arginine uptake without impairing overall transport activity, indicating His544 is not directly involved in substrate binding; two SLC38A9 structures at high and low pH reveal the structural basis of pH-induced activation.\",\n      \"method\": \"Transport assays at different pH, site-directed mutagenesis of His544, cryo-EM/structural comparison at two pH values\",\n      \"journal\": \"FEBS Letters / bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro transport assay with mutagenesis and structural comparison, single lab, peer-reviewed publication\",\n      \"pmids\": [\"42070976\", \"41279478\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SLC38A9 is a lysosomal 11-pass transmembrane transporter and arginine sensor that physically associates with the Ragulator–Rag GTPase complex; upon arginine binding, it acts as a GEF to load RagA with GTP and destabilizes the inhibitory folliculin complex (LFC) to release FLCN:FNIP2 GAP activity toward RagC, collectively driving the Rag GTPases into their active state and recruiting mTORC1 to the lysosomal surface; it also mediates arginine-regulated efflux of essential amino acids (including leucine) from lysosomes to sustain cytosolic mTORC1 activation, senses lysosomal cholesterol through conserved motifs in a complex with NPC1, and its transport activity is further regulated by lysosomal pH through the His544 residue.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SLC38A9 is a multi-pass lysosomal transmembrane transporter that serves as an amino acid sensor coupling lysosomal nutrient content to mTORC1 activation [#0, #1]. It physically associates with the Rag GTPase–Ragulator machinery at the lysosomal membrane in an amino-acid-sensitive, nucleotide-state-dependent manner, and acts upstream of the Rag GTPases: its loss blocks amino-acid (especially arginine)-induced mTORC1 activation, while overexpression renders mTORC1 signaling resistant to amino acid withdrawal [#0, #1, #2]. Mechanistically, arginine binding converts SLC38A9 into a guanine nucleotide exchange factor that loads RagA with GTP, and its cytoplasmic tail destabilizes the inhibitory folliculin complex to release FLCN:FNIP2 GAP activity toward RagC, together driving the Rag heterodimer to its active conformation [#5, #8]. Beyond sensing, SLC38A9 functions as a transporter that effluxes essential amino acids including leucine from lysosomes in an arginine-regulated fashion, enabling leucine generated by lysosomal proteolysis to exit and sustain mTORC1; this efflux activity is required for pancreatic cancer cells to use macropinocytosed protein for tumor growth [#3]. Structural studies of the arginine-bound transporter define a conserved WNTMM motif essential for arginine transport [#6], and reconstitution shows cooperative glutamine and arginine transport with a Na+ site at T453, cholesterol-stimulated activity, and arginine acting as a modulator of glutamine efflux [#7]. SLC38A9 additionally links lysosomal cholesterol to mTORC1 through conserved cholesterol-responsive motifs and a complex with NPC1, independently of its arginine-sensing function [#4]. Its arginine transport is further gated by lysosomal pH via the protonation state of His544 [#15].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Established the identity of the lysosomal amino acid sensor feeding mTORC1: before this, how amino acids signaled to the Rag GTPases at the lysosome was unknown.\",\n      \"evidence\": \"Reciprocal Co-IP, amino acid transport assays, and loss/gain-of-function epistasis with mTORC1 readouts placing SLC38A9 upstream of the Rags, replicated across labs\",\n      \"pmids\": [\"25567906\", \"25561175\", \"25963655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the biochemical mechanism by which SLC38A9 activates the Rag GTPases\", \"High Km arginine transport left the physiological transport substrate and direction unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved what SLC38A9 actually transports physiologically, showing it effluxes essential amino acids including leucine from lysosomes to sustain mTORC1 and support nutrient scavenging.\",\n      \"evidence\": \"Isotope-tracing transport assays, lysosome immunopurification, and knockout cells with tumor-formation readouts in pancreatic cancer\",\n      \"pmids\": [\"29053970\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not separate transport-dependent from sensing-dependent contributions to mTORC1 in all contexts\", \"Mechanism coupling efflux to Rag activation not structurally defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended SLC38A9 sensing beyond amino acids by showing it conveys a lysosomal cholesterol signal to mTORC1 in complex with NPC1.\",\n      \"evidence\": \"Reciprocal Co-IP of SLC38A9–NPC1, mutagenesis of cholesterol-responsive motifs, and cholesterol depletion/repletion with mTORC1 readouts\",\n      \"pmids\": [\"28336668\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of cholesterol recognition not determined\", \"Relationship between cholesterol sensing and transport conformational cycle unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined the biochemical activity behind Rag activation, showing SLC38A9 is an arginine-stimulated GEF that loads RagA with GTP.\",\n      \"evidence\": \"In vitro nucleotide-exchange GEF assays with reconstituted Rag GTPases and arginine-binding experiments\",\n      \"pmids\": [\"30181260\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not provide structural snapshots of the SLC38A9–Rag intermediate\", \"GEF activity toward RagA vs Ragulator GEF toward RagC integration not fully reconstituted\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided the atomic basis of arginine recognition by the transporter, identifying the WNTMM motif required for transport.\",\n      \"evidence\": \"X-ray crystal structure of zebrafish SLC38A9 in cytosol-open state bound to arginine with site-directed mutagenesis and transport assays\",\n      \"pmids\": [\"29872228\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Single conformational state captured; full transport cycle not visualized\", \"Human protein structure not solved in this work\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Reconstituted the human transporter to define substrate kinetics, ion coupling, and the distinct roles of arginine and glutamine.\",\n      \"evidence\": \"Proteoliposome transport assays, mutagenesis identifying a Na+ site at T453, and N-terminal deletion analysis\",\n      \"pmids\": [\"31295473\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological relevance of glutamine efflux vs arginine modulation in cells not established\", \"Two-site binding model for glutamine and arginine inferred but not structurally confirmed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Explained mechanistically how the cytoplasmic tail activates Rags by destabilizing the inhibitory folliculin complex to trigger FLCN:FNIP2 GAP activity toward RagC.\",\n      \"evidence\": \"Cryo-EM structures of Rags–Ragulator–SLC38A9 tail in pre- and post-GTP-hydrolysis states with in vitro GAP assays\",\n      \"pmids\": [\"32868926\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How arginine occupancy of the transmembrane domain is communicated to the cytoplasmic tail not resolved\", \"Single-lab structural model\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Mapped additional lysosomal interaction partners and transcriptional control, linking SLC38A9 to SLC36A1 and to ATF4-driven amino acid response regulation.\",\n      \"evidence\": \"Co-IP and co-localization with SLC36A1 in C2C12 cells; promoter/AARE binding analysis and ATF4 knockdown in porcine muscle cells\",\n      \"pmids\": [\"34572527\", \"34246831\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of SLC36A1–SLC38A9 mutual stabilization not mechanistically dissected\", \"ATF4 regulation shown in single species without conservation testing\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified roles for SLC38A9 in viral entry and a transport-independent lysosome-positioning function, broadening its cellular involvement.\",\n      \"evidence\": \"Co-IP with SARS-CoV-2 S1 and HIV-1 Tat basic domains plus functional knockdown; high-content lysosome-positioning imaging along a BORC–kinesin axis (preprint)\",\n      \"pmids\": [\"39071889\", \"40324823\", \"bio_10.1101_2024.10.12.618047\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Lysosome-dispersal axis is preprint and not biochemically validated\", \"Pathogen-protein interactions are single-lab with limited mechanistic depth\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed lysosomal pH gates SLC38A9 transport through a defined histidine sensor, connecting organelle pH to nutrient sensing.\",\n      \"evidence\": \"Transport assays at varying pH, His544 mutagenesis, and structural comparison at high and low pH\",\n      \"pmids\": [\"42070976\", \"41279478\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological impact of pH gating on mTORC1 output not tested in cells\", \"Single-lab structural and functional dataset\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the transmembrane substrate-binding events (arginine, glutamine, cholesterol, pH) are integrated and conformationally transmitted to the cytoplasmic GEF/LFC-destabilizing tail to time Rag activation remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No full-length human structure coupling transport state to Rag-activation state\", \"Quantitative contribution of transport vs sensing to mTORC1 in vivo not separated\", \"Integration of cholesterol and pH signals with arginine sensing not mechanistically unified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 3, 6, 7]},\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [0, 4, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 8]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2, 5, 8]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"complexes\": [\"Rag GTPase–Ragulator complex\", \"lysosomal folliculin complex (LFC)\"],\n    \"partners\": [\"RagA\", \"RagC\", \"Ragulator\", \"FLCN\", \"FNIP2\", \"NPC1\", \"SLC36A1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}