{"gene":"RRAGB","run_date":"2026-04-28T20:42:06","timeline":{"discoveries":[{"year":2008,"finding":"RagB (RRAGB), as part of the heterodimeric Rag GTPase complex, binds raptor (a component of mTORC1) in an amino acid-sensitive manner and is necessary for activation of the mTORC1 pathway by amino acids. A constitutively GTP-bound RagB mutant made mTORC1 resistant to amino acid deprivation, while a GDP-bound mutant prevented amino acid stimulation of mTORC1. The Rag proteins promote intracellular localization of mTOR to a lysosomal compartment containing Rheb without directly stimulating mTORC1 kinase activity.","method":"Co-immunoprecipitation, dominant-active/dominant-negative GTPase mutants, subcellular localization imaging","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP and GTPase mutant epistasis, foundational study replicated extensively","pmids":["18497260"],"is_preprint":false},{"year":2010,"finding":"The Rag GTPases (including RagB/RRAGB) reside on lysosomal membranes via the Ragulator complex (encoded by MAPKSP1, ROBLD3, c11orf59), which recruits the Rags to lysosomes. Amino acids induce mTORC1 movement to lysosomal membranes where active Rag heterodimers reside. Constitutive targeting of mTORC1 to lysosomes rendered mTORC1 amino acid-insensitive and Rag/Ragulator-independent but still Rheb-dependent, placing Rag-Ragulator-mediated lysosomal translocation as the key event in amino acid signaling.","method":"Co-immunoprecipitation, lysosomal localization imaging, epistasis with constitutively lysosome-targeted mTORC1","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, constitutive targeting epistasis, widely replicated","pmids":["20381137"],"is_preprint":false},{"year":2012,"finding":"Ragulator functions as a guanine nucleotide exchange factor (GEF) for RagA and RagB (RRAGB), stimulating GTP loading of these GTPases in response to amino acids in a v-ATPase-dependent fashion. Two additional Ragulator components (HBXIP and C7orf59) were identified as required for mTORC1 activation by amino acids.","method":"In vitro GEF assay, Co-immunoprecipitation, nucleotide loading assays, genetic knockdown","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — in vitro biochemical GEF activity assay plus cell-based validation, replicated","pmids":["22980980"],"is_preprint":false},{"year":2012,"finding":"Glutaminolysis (conversion of glutamine to α-ketoglutarate) activates mTORC1 upstream of the Rag GTPases by promoting GTP loading of RagB and lysosomal translocation of mTORC1. Inhibition of glutaminolysis prevented RagB GTP loading; constitutively active Rag heterodimer rescued mTORC1 activation in absence of glutaminolysis, placing RagB downstream of α-ketoglutarate production.","method":"Nucleotide loading assays for RagB, epistasis with constitutively active Rag heterodimer, lysosomal translocation imaging","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 1-2 — direct RagB GTP loading measured, constitutively active Rag epistasis, multiple methods","pmids":["22749528"],"is_preprint":false},{"year":2012,"finding":"Leucyl-tRNA synthetase (LRS) functions as a GAP (GTPase-activating protein) for Rag GTPases (including RagB/RRAGB) in response to intracellular leucine, binding directly to the Rag GTPase in an amino acid-dependent manner to activate mTORC1 signaling.","method":"In vitro GAP assay, Co-immunoprecipitation, mutagenesis of leucine-binding residues of LRS","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — in vitro GAP activity demonstrated, leucine-binding site mutagenesis, direct binding shown","pmids":["22424946"],"is_preprint":false},{"year":2011,"finding":"p62/SQSTM1 binds the Rag GTPases (including RagB/RRAGB) in an amino acid-dependent manner, favors formation of the active Rag heterodimer stabilized by raptor, colocalizes with Rags at the lysosomal compartment, and is required for mTORC1 interaction with Rag GTPases and for mTORC1 translocation to the lysosome.","method":"Co-immunoprecipitation, co-localization imaging, amino acid-dependent interaction assays, knockdown with mTORC1 activation readouts","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, localization, and functional epistasis in multiple cell contexts","pmids":["21981924"],"is_preprint":false},{"year":2013,"finding":"GATOR1 (composed of DEPDC5, Nprl2, Nprl3) has GTPase-activating protein (GAP) activity toward RagA and RagB (RRAGB), functioning as a negative regulator of Rag GTPases and hence mTORC1. Inactivating mutations in GATOR1 components in human cancers cause mTORC1 hyperactivation and amino acid insensitivity.","method":"In vitro GAP assay, cancer cell line GATOR1 knockdown, amino acid starvation epistasis, mutant analysis","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro GAP activity demonstrated for RagA/B, cancer mutation analysis, widely replicated","pmids":["23723238"],"is_preprint":false},{"year":2000,"finding":"RagC and RagD were identified as novel GTP-binding proteins that interact with RagA and RagB (RRAGB) via their C-terminal regions (containing a leucine zipper and coiled-coil structure). RagC/D associated with both GDP- and GTP-bound forms of RagA. RagC and RagD changed their subcellular localization depending on the nucleotide-bound state of RagA, establishing the RagA/B–RagC/D heterodimer paradigm.","method":"Yeast two-hybrid, GST pulldown, radiolabeled GTP/GDP binding assay, subcellular localization studies","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro GTP binding, pulldown, and localization studies; foundational discovery of Rag heterodimer","pmids":["11073942"],"is_preprint":false},{"year":2013,"finding":"Folliculin (FLCN) is recruited to lysosomal surfaces upon amino acid depletion and directly binds RagA/B (including RRAGB) via its GTPase domain, and together with FNIP1 promotes amino acid-dependent mTORC1 recruitment to lysosomes via Rag GTPases.","method":"Co-immunoprecipitation, lysosomal localization imaging, amino acid starvation/stimulation assays, FLCN knockout/knockdown","journal":"Journal of Cell Biology","confidence":"High","confidence_rationale":"Tier 2 — direct binding to RagA/B demonstrated, lysosomal recruitment shown, functional epistasis","pmids":["24081491"],"is_preprint":false},{"year":2014,"finding":"Sestrins bind the heterodimeric RagA/B–RagC/D GTPases and function as guanine nucleotide dissociation inhibitors (GDIs) for RagA/B (including RRAGB), inhibiting amino acid-induced Rag guanine nucleotide exchange and mTORC1 lysosomal translocation. A conserved GDI motif is required; its mutation creates dominant-negative Sestrin rendering mTORC1 insensitive to amino acid deprivation.","method":"Co-immunoprecipitation, in vitro GDI assay, mutagenesis of GDI motif, cell-permeable peptide inhibition, mouse knockout","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — in vitro GDI activity demonstrated, GDI motif mutagenesis, mouse model validation","pmids":["25259925"],"is_preprint":false},{"year":2015,"finding":"SLC38A9, a lysosomal transmembrane amino acid transporter, interacts with Rag GTPases (including RRAGB) and Ragulator in an amino acid-sensitive manner, transporting arginine with high Km. Loss of SLC38A9 represses mTORC1 activation by amino acids (particularly arginine); overexpression of its Ragulator-binding domain renders mTORC1 insensitive to amino acid starvation but not to Rag activity, placing SLC38A9 upstream of the Rag GTPases.","method":"Co-immunoprecipitation, amino acid transport assays, lysosomal localization imaging, loss-of-function and gain-of-function genetic epistasis","journal":"Science","confidence":"High","confidence_rationale":"Tier 1-2 — transport assay, direct interaction with Rag GTPases, epistasis upstream of Rags; replicated in parallel Nature paper","pmids":["25567906","25561175"],"is_preprint":false},{"year":2017,"finding":"SZT2 recruits a fraction of GATOR1 and GATOR2 to form a SZT2-orchestrated GATOR (SOG) complex essential for GATOR- and Sestrin-dependent nutrient sensing and mTORC1 regulation via Rag GTPases (including RRAGB). SZT2 deficiency causes constitutive mTORC1 signaling under nutrient deprivation; lysosomal localization of SOG is required for its function.","method":"Co-immunoprecipitation, lysosomal localization, genetic knockout mouse, epistasis with GATOR1/GATOR2 overexpression","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, mouse knockout, and functional epistasis; independent study","pmids":["28199315"],"is_preprint":false},{"year":2018,"finding":"TRIM37 interacts with mTOR and RRAGB, enhances the mTOR–RRAGB interaction, and promotes lysosomal localization of mTOR, thereby activating amino acid-stimulated mTORC1 signaling. Loss of TRIM37 reduces TFEB phosphorylation, causing its nuclear translocation and transcriptional activation of lysosome biogenesis and autophagy genes.","method":"Co-immunoprecipitation, lysosomal localization imaging, TRIM37 knockdown/knockout, TFEB phosphorylation and nuclear translocation assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and localization with functional readouts; single lab study","pmids":["29940807"],"is_preprint":false},{"year":2022,"finding":"NUFIP2 contributes to mTOR inactivation (via the Ragulator-RRAGA-RRAGB complex) together with LGALS8 (galectin-8) at the lysosome following lysosomal damage. GABARAPs interact directly with NUFIP2 and are required (via Atg8ylation) for NUFIP2 recruitment to damaged lysosomes, where it inhibits the Rag GTPase complex.","method":"Proteomic studies of damaged lysosomes, Co-immunoprecipitation, lysosome immunopurification (LysoIP), mTOR activity assays, GABARAP knockout","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2-3 — proteomics + Co-IP + functional mTOR readout; single lab study","pmids":["36394332"],"is_preprint":false},{"year":2022,"finding":"circEXOC6B (a circular RNA) inhibits the heterodimer formation of RRAGB by directly binding to it, thereby suppressing mTORC1 pathway activity. HIF1A transcriptionally upregulates RRAGB by binding to its promoter, creating a HIF1A-RRAGB-mTORC1 positive feedback loop in colorectal cancer that circEXOC6B can interrupt.","method":"RNA pull-down, RNA-binding protein immunoprecipitation, Co-immunoprecipitation, chromatin immunoprecipitation, dual-luciferase assay, in vivo xenograft","journal":"Molecular Cancer","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple orthogonal RNA-protein interaction assays plus ChIP; single lab, circRNA context","pmids":["35739524"],"is_preprint":false},{"year":2023,"finding":"RRAGB overexpression in glioblastoma cells reduces proliferation, migration, and invasion and induces G0/G1 cell cycle arrest. RRAGB upregulation decreases expression of PI3K, phosphorylated AKT, mTOR, and S6K; restoring AKT activation rescues GBM cell proliferative and invasive properties, indicating RRAGB suppresses GBM progression partly through blockade of the PI3K/AKT signaling axis.","method":"RRAGB overexpression in GBM cell lines, western blot for PI3K/AKT/mTOR/S6K, AKT activator rescue experiment, xenograft and orthotopic mouse models","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2-3 — gain-of-function with pathway rescue experiment and in vivo validation; single lab","pmids":["37517217"],"is_preprint":false},{"year":2024,"finding":"RRAGB is a target of miR-21-3p in endothelial progenitor cells (EPCs); overexpression of RRAGB activates the mTOR pathway, inhibits autophagic activity, and impairs EPC proliferation, migration, and tube formation. Berberine downregulates RRAGB through upregulation of miR-21-3p, restoring EPC function and promoting wound healing.","method":"Luciferase reporter assay (miR-21-3p/RRAGB targeting), RRAGB overexpression in EPCs, western blot for mTOR/autophagy markers, EPC functional assays, DVT mouse model","journal":"Regenerative Therapy","confidence":"Low","confidence_rationale":"Tier 3 — single lab, indirect (miRNA-mediated) RRAGB manipulation without direct biochemical characterization","pmids":["39100534"],"is_preprint":false},{"year":2025,"finding":"CircMRP4 acts as a sponge for miR-499-5p, leading to upregulation of RRAGB and consequent activation of mTORC1/P70S6K signaling in podocytes under high glucose conditions, promoting podocyte apoptosis and inflammation in diabetic kidney disease.","method":"Dual-luciferase reporter, RNA immunoprecipitation, RNA pull-down, RRAGB expression/knockdown, mTORC1/P70S6K western blot, in vivo DKD mouse model","journal":"Cellular Signalling","confidence":"Low","confidence_rationale":"Tier 3 — indirect (circRNA/miRNA-mediated) manipulation of RRAGB; single lab","pmids":["39842531"],"is_preprint":false}],"current_model":"RRAGB (RagB) is a Ras-family small GTPase that forms obligate heterodimers with RagC or RagD and functions as a central node in amino acid sensing to mTORC1: when GTP-loaded (stimulated by Ragulator acting as its GEF, leucyl-tRNA synthetase acting as a Rag GAP, and regulated by GATOR1 GAP activity and Sestrin GDI activity), the RagA/B–RagC/D heterodimer recruits mTORC1 to lysosomal membranes where it is activated by Rheb, while upstream sensors including SLC38A9 (arginine), glutaminolysis (α-ketoglutarate), FLCN, p62, NUFIP2, and TRIM37 modulate this process; RRAGB also suppresses PI3K/AKT signaling in certain tumor contexts and is subject to transcriptional regulation by HIF1A and post-transcriptional regulation by miRNAs."},"narrative":{"teleology":[{"year":2000,"claim":"Identification of RagC/D as obligate heterodimeric partners of RagA/B established the fundamental Rag GTPase architecture, resolving how these atypical small GTPases are organized.","evidence":"Yeast two-hybrid, GST pulldown, and GTP/GDP binding assays in mammalian cells","pmids":["11073942"],"confidence":"High","gaps":["No upstream regulation or downstream effector identified at this stage","Functional relevance of heterodimer to signaling pathways unknown"]},{"year":2008,"claim":"Linking RagB GTP loading to amino acid-dependent mTORC1 activation and lysosomal translocation revealed the core physiological function of the Rag GTPases, answering what signal they relay and to whom.","evidence":"Co-IP of Rag–Raptor, constitutively active/dominant-negative RagB mutants, mTOR lysosomal localization imaging","pmids":["18497260"],"confidence":"High","gaps":["Mechanism anchoring Rag GTPases to lysosomes unknown","Identity of the RagB GEF and GAP unresolved"]},{"year":2010,"claim":"Discovery that the Ragulator complex tethers Rag GTPases to lysosomes and that constitutive lysosomal targeting of mTORC1 bypasses Rag/Ragulator dependence established lysosomal recruitment as the rate-limiting step in amino acid sensing.","evidence":"Co-IP, lysosomal localization imaging, constitutively lysosome-targeted mTORC1 epistasis","pmids":["20381137"],"confidence":"High","gaps":["Whether Ragulator has catalytic activity toward Rag GTPases undetermined","Upstream amino acid sensors unidentified"]},{"year":2011,"claim":"Identification of p62/SQSTM1 as an amino acid-dependent binding partner of Rag GTPases that stabilizes the active heterodimer and promotes mTORC1 lysosomal recruitment added a regulatory scaffold component to the pathway.","evidence":"Co-IP, co-localization imaging, amino acid-dependent interaction assays, knockdown with mTORC1 readouts","pmids":["21981924"],"confidence":"High","gaps":["Precise mechanism by which p62 stabilizes the active Rag configuration unclear","Relationship to p62's role in autophagy not dissected"]},{"year":2012,"claim":"Three concurrent discoveries defined the enzymology governing RagB nucleotide state: Ragulator as the GEF, leucyl-tRNA synthetase as a leucine-sensing GAP, and glutaminolysis/α-ketoglutarate as an upstream signal promoting RagB GTP loading.","evidence":"In vitro GEF assay for Ragulator, in vitro GAP assay for LRS with leucine-binding mutagenesis, RagB nucleotide loading assays with glutaminolysis inhibition and constitutively active Rag rescue","pmids":["22980980","22424946","22749528"],"confidence":"High","gaps":["Structural basis of Ragulator GEF activity unresolved","LRS GAP activity questioned by later studies regarding specificity for RagD vs RagB","How α-ketoglutarate mechanistically influences RagB GTP loading unclear"]},{"year":2013,"claim":"Identification of GATOR1 as a RagA/B GAP and FLCN as a direct RagA/B-binding protein defined key negative and positive regulators converging on Rag nucleotide cycling, and linked GATOR1 loss-of-function to cancer.","evidence":"In vitro GAP assay for GATOR1 on RagA/B, cancer cell line GATOR1 knockdown; Co-IP of FLCN with RagA/B, FLCN knockout epistasis","pmids":["23723238","24081491"],"confidence":"High","gaps":["Whether FLCN has direct catalytic activity toward Rag GTPases unresolved at this point","Structural basis of GATOR1 GAP mechanism unknown"]},{"year":2014,"claim":"Demonstration that Sestrins act as GDIs for RagA/B revealed a distinct inhibitory mechanism—blocking nucleotide exchange rather than stimulating GTP hydrolysis—adding a new regulatory modality to the pathway.","evidence":"In vitro GDI assay, GDI motif mutagenesis, cell-permeable peptide inhibition, mouse knockout","pmids":["25259925"],"confidence":"High","gaps":["How Sestrin GDI activity is itself regulated by stress signals incompletely understood","Whether Sestrins have additional Rag-independent functions in mTORC1 regulation unclear"]},{"year":2015,"claim":"SLC38A9 was identified as a lysosomal arginine sensor upstream of Rag GTPases, providing the first mechanistic link between a specific amino acid transporter and the Rag-mTORC1 pathway.","evidence":"Co-IP of SLC38A9 with Rag GTPases and Ragulator, arginine transport assay, loss-of-function and gain-of-function epistasis","pmids":["25567906","25561175"],"confidence":"High","gaps":["How SLC38A9 mechanistically alters Rag nucleotide state not determined","Whether SLC38A9 senses luminal arginine directly or indirectly debated"]},{"year":2017,"claim":"Discovery that SZT2 organizes GATOR1/GATOR2 into the SOG complex at lysosomes explained how GATOR-mediated Rag regulation is spatially coordinated, resolving how nutrient-insensitive mTORC1 signaling arises from SZT2 deficiency.","evidence":"Co-IP, lysosomal localization, genetic knockout mouse, GATOR1/2 epistasis","pmids":["28199315"],"confidence":"High","gaps":["Whether SZT2 has additional scaffolding roles beyond GATOR complex organization unknown","Structural basis of SOG complex assembly unresolved"]},{"year":2018,"claim":"TRIM37 was shown to enhance the mTOR–RRAGB interaction and promote mTOR lysosomal localization, identifying a new positive regulator that also connects Rag-mTORC1 signaling to TFEB-dependent lysosome biogenesis.","evidence":"Co-IP of TRIM37 with mTOR and RRAGB, lysosomal localization imaging, TFEB phosphorylation assays","pmids":["29940807"],"confidence":"Medium","gaps":["Whether TRIM37's E3 ligase activity is required for its effect on RRAGB not established","Single-lab finding awaiting independent replication"]},{"year":2022,"claim":"Two studies expanded the regulatory landscape: NUFIP2/galectin-8 were found to inactivate the Rag complex at damaged lysosomes, and circEXOC6B was shown to directly bind RRAGB to inhibit heterodimer formation, while HIF1A was identified as a transcriptional activator of RRAGB.","evidence":"LysoIP proteomics, Co-IP, mTOR activity assays for NUFIP2; RNA pull-down, RIP, ChIP, dual-luciferase, xenograft for circEXOC6B/HIF1A","pmids":["36394332","35739524"],"confidence":"Medium","gaps":["Mechanism by which NUFIP2 inhibits Rag nucleotide state not biochemically defined","circEXOC6B binding site on RRAGB uncharacterized","HIF1A–RRAGB transcriptional axis not validated outside colorectal cancer"]},{"year":2023,"claim":"RRAGB overexpression was shown to suppress glioblastoma cell proliferation via PI3K/AKT pathway inhibition, revealing a context-dependent tumor-suppressive function distinct from its canonical mTORC1-activating role.","evidence":"RRAGB overexpression in GBM cell lines, PI3K/AKT/mTOR/S6K western blot, AKT activator rescue, xenograft and orthotopic models","pmids":["37517217"],"confidence":"Medium","gaps":["Mechanism by which RRAGB suppresses PI3K/AKT unclear—may be indirect via mTORC1 negative feedback","Not reconciled with RagB's canonical role in mTORC1 activation","Single lab, single cancer type"]},{"year":null,"claim":"How RRAGB's tumor-suppressive activity via PI3K/AKT inhibition is mechanistically reconciled with its canonical role in mTORC1 activation, and whether RRAGB mutations contribute to human Mendelian disease or are recurrently altered in cancer, remain open questions.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of full-length human RagB–RagC/D heterodimer bound to effectors","No direct disease-causing mutations in RRAGB reported","Context-dependent pro- versus anti-proliferative roles not mechanistically resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,2,3,4,6,7,9]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,1,2,5,8,10,11,13]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2,3,4,6,9,10,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[12,13]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3,10,11]}],"complexes":["Rag GTPase heterodimer (RagA/B–RagC/D)","Rag–Ragulator complex"],"partners":["RRAGC","RRAGD","RPTOR","LAMTOR1","DEPDC5","FLCN","SQSTM1","SESN2"],"other_free_text":[]},"mechanistic_narrative":"RRAGB (RagB) is a Ras-family small GTPase that forms obligate heterodimers with RagC or RagD and serves as a central mediator of amino acid signaling to mTORC1, coupling nutrient availability to cell growth [PMID:18497260, PMID:11073942]. In response to amino acids, RagB is loaded with GTP through the guanine nucleotide exchange activity of the lysosome-anchored Ragulator complex, while leucyl-tRNA synthetase and GATOR1 act as GAPs, and Sestrins function as GDIs to negatively regulate its activation; the active RagB–RagC/D heterodimer recruits mTORC1 to lysosomal membranes where it is activated by Rheb [PMID:22980980, PMID:22424946, PMID:23723238, PMID:25259925, PMID:20381137]. Upstream nutrient inputs including arginine sensing via the lysosomal transporter SLC38A9, glutaminolysis-derived α-ketoglutarate, folliculin (FLCN), p62/SQSTM1, and the SZT2-organized GATOR complex converge on the RagB nucleotide cycle to tune mTORC1 activation [PMID:25567906, PMID:22749528, PMID:24081491, PMID:21981924, PMID:28199315]. RRAGB overexpression in glioblastoma cells suppresses proliferation through inhibition of PI3K/AKT signaling, and HIF1A transcriptionally upregulates RRAGB, indicating additional regulatory and context-dependent roles in cancer biology [PMID:37517217, PMID:35739524]."},"prefetch_data":{"uniprot":{"accession":"Q5VZM2","full_name":"Ras-related GTP-binding protein B","aliases":[],"length_aa":374,"mass_kda":43.2,"function":"Guanine nucleotide-binding protein that plays a crucial role in the cellular response to amino acid availability through regulation of the mTORC1 signaling cascade (PubMed:18497260, PubMed:20381137, PubMed:23723238, PubMed:24095279). Forms heterodimeric Rag complexes with RagC/RRAGC or RagD/RRAGD and cycles between an inactive GDP-bound and an active GTP-bound form: RagB/RRAGB is in its active form when GTP-bound RagB/RRAGB forms a complex with GDP-bound RagC/RRAGC (or RagD/RRAGD) and in an inactive form when GDP-bound RagB/RRAGB heterodimerizes with GTP-bound RagC/RRAGC (or RagD/RRAGD) (PubMed:18497260, PubMed:20381137, PubMed:23723238, PubMed:24095279). In its GTP-bound active form, promotes the recruitment of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB (PubMed:18497260, PubMed:20381137, PubMed:23723238). Involved in the RCC1/Ran-GTPase pathway (PubMed:9394008)","subcellular_location":"Cytoplasm; Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q5VZM2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RRAGB","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RRAGB","total_profiled":1310},"omim":[{"mim_id":"618834","title":"LATE ENDOSOMAL/LYSOSOMAL ADAPTOR, MAPK AND MTOR ACTIVATOR 4; LAMTOR4","url":"https://www.omim.org/entry/618834"},{"mim_id":"616599","title":"BLOC1-RELATED COMPLEX, SUBUNIT 6; BORCS6","url":"https://www.omim.org/entry/616599"},{"mim_id":"616203","title":"SOLUTE CARRIER FAMILY 38, MEMBER 9; SLC38A9","url":"https://www.omim.org/entry/616203"},{"mim_id":"608521","title":"LATE ENDOSOMAL/LYSOSOMAL ADAPTOR, MAPK AND MTOR ACTIVATOR 5; LAMTOR5","url":"https://www.omim.org/entry/608521"},{"mim_id":"300725","title":"RAS-RELATED GTP-BINDING PROTEIN B; RRAGB","url":"https://www.omim.org/entry/300725"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RRAGB"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q5VZM2","domains":[{"cath_id":"3.40.50.300","chopping":"38-69_104-239","consensus_level":"high","plddt":94.0865,"start":38,"end":239},{"cath_id":"3.30.450.190","chopping":"244-361","consensus_level":"high","plddt":93.5654,"start":244,"end":361}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VZM2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VZM2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VZM2-F1-predicted_aligned_error_v6.png","plddt_mean":81.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RRAGB","jax_strain_url":"https://www.jax.org/strain/search?query=RRAGB"},"sequence":{"accession":"Q5VZM2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5VZM2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5VZM2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VZM2"}},"corpus_meta":[{"pmid":"25651471","id":"PMC_25651471","title":"Dichotomy of Genetic Abnormalities in PEComas With Therapeutic Implications.","date":"2015","source":"The American journal of surgical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/25651471","citation_count":189,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29940807","id":"PMC_29940807","title":"TRIM37 deficiency induces autophagy through deregulating the MTORC1-TFEB axis.","date":"2018","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/29940807","citation_count":37,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35739524","id":"PMC_35739524","title":"circEXOC6B interacting with RRAGB, an mTORC1 activator, inhibits the progression of colorectal cancer by antagonizing the HIF1A-RRAGB-mTORC1 positive feedback loop.","date":"2022","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35739524","citation_count":33,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15202009","id":"PMC_15202009","title":"Identification and characterization 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Loss of TRIM37 reduces TFEB phosphorylation, causing TFEB nuclear translocation and transcriptional activation of autophagy/lysosome biogenesis genes.\",\n      \"method\": \"Co-immunoprecipitation, lysosomal localization assays, phosphorylation analysis, siRNA knockdown with functional readouts (autophagy induction, TFEB translocation)\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP showing TRIM37-RRAGB-MTOR complex, combined with functional localization and phosphorylation readouts in a single study\",\n      \"pmids\": [\"29940807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"circEXOC6B binds directly to RRAGB and inhibits RRAGB heterodimer formation, thereby suppressing the mTORC1 pathway and reducing HIF1A levels. HIF1A in turn upregulates RRAGB transcription by binding to the RRAGB promoter, forming a HIF1A-RRAGB-mTORC1 positive feedback loop in colorectal cancer.\",\n      \"method\": \"RNA pull-down, mass spectrometry, RNA-binding protein immunoprecipitation, co-immunoprecipitation, chromatin immunoprecipitation, dual-luciferase assay, FISH, immunofluorescence, western blot\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (RNA pulldown, Co-IP, ChIP, luciferase) establishing direct binding and functional consequence\",\n      \"pmids\": [\"35739524\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NUFIP2 contributes to MTORC1 inactivation at the lysosome together with LGALS8 (galectin 8) via the Ragulator-RRAGA-RRAGB complex following lysosomal damage; GABARAP-mediated membrane Atg8ylation is required for recruitment of NUFIP2 to damaged lysosomes to engage this RRAGB-containing complex.\",\n      \"method\": \"Proteomic studies (lysosome immunopurification), co-immunoprecipitation, genetic knockdown with MTORC1 activity readout, lysosomal damage assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — proteomics plus Co-IP and functional KD, but RRAGB role is partially inferred within the Ragulator complex context\",\n      \"pmids\": [\"36394332\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RRAGB overexpression in glioblastoma cells suppresses proliferation, migration, and invasion and induces G0/G1 cell cycle arrest; mechanistically, RRAGB upregulation decreases PI3K expression, phospho-AKT, mTOR, and S6K levels, and AKT activation rescues the anti-cancer phenotype, indicating RRAGB acts upstream of the PI3K/AKT/mTOR axis in GBM.\",\n      \"method\": \"Overexpression and knockdown in GBM cell lines, western blot for PI3K/p-AKT/mTOR/S6K, AKT activator rescue experiments, xenograft and orthotopic mouse models\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO/OE with defined cellular and molecular phenotype plus epistasis rescue experiment, single lab study\",\n      \"pmids\": [\"37517217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"miR-21-3p directly targets RRAGB (confirmed by luciferase reporter assay); RRAGB overexpression activates the mTOR pathway, inhibits autophagic activity, and impairs endothelial progenitor cell (EPC) function including proliferation, migration, and tube formation. Berberine upregulates miR-21-3p, thereby suppressing RRAGB and restoring EPC function.\",\n      \"method\": \"Luciferase reporter assay, western blot (mTOR pathway and autophagy markers), overexpression and knockdown in EPCs, CCK-8, Transwell, tube formation assays, DVT mouse model\",\n      \"journal\": \"Regenerative therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct target validation by luciferase plus functional overexpression readout, single lab\",\n      \"pmids\": [\"39100534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"circMRP4 acts as a sponge for miR-499-5p, leading to upregulation of RRAGB, which activates mTORC1/P70S6K signaling and promotes podocyte apoptosis and inflammation under high-glucose conditions in diabetic kidney disease.\",\n      \"method\": \"Dual-luciferase reporter, RNA immunoprecipitation, RNA pull-down, knockdown and overexpression assays, western blot for mTORC1/P70S6K pathway\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple biochemical methods confirming sponge relationship and RRAGB-mTORC1 link, single lab\",\n      \"pmids\": [\"39842531\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RRAGB (RagB) is a Ras-related GTPase that functions as part of the Ragulator-Rag heterodimer complex at the lysosomal surface to activate mTORC1 signaling in response to amino acid availability; it is positively regulated by TRIM37 (which enhances MTOR-RRAGB interaction and lysosomal MTOR localization) and negatively regulated by circRNA sponges (circEXOC6B, circMRP4) and miRNAs (miR-21-3p, miR-499-5p) that suppress its expression, while also acting upstream of PI3K/AKT to suppress tumor cell growth in some contexts.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"RagB (RRAGB), as part of the heterodimeric Rag GTPase complex, binds raptor (a component of mTORC1) in an amino acid-sensitive manner and is necessary for activation of the mTORC1 pathway by amino acids. A constitutively GTP-bound RagB mutant made mTORC1 resistant to amino acid deprivation, while a GDP-bound mutant prevented amino acid stimulation of mTORC1. The Rag proteins promote intracellular localization of mTOR to a lysosomal compartment containing Rheb without directly stimulating mTORC1 kinase activity.\",\n      \"method\": \"Co-immunoprecipitation, dominant-active/dominant-negative GTPase mutants, subcellular localization imaging\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP and GTPase mutant epistasis, foundational study replicated extensively\",\n      \"pmids\": [\"18497260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The Rag GTPases (including RagB/RRAGB) reside on lysosomal membranes via the Ragulator complex (encoded by MAPKSP1, ROBLD3, c11orf59), which recruits the Rags to lysosomes. Amino acids induce mTORC1 movement to lysosomal membranes where active Rag heterodimers reside. Constitutive targeting of mTORC1 to lysosomes rendered mTORC1 amino acid-insensitive and Rag/Ragulator-independent but still Rheb-dependent, placing Rag-Ragulator-mediated lysosomal translocation as the key event in amino acid signaling.\",\n      \"method\": \"Co-immunoprecipitation, lysosomal localization imaging, epistasis with constitutively lysosome-targeted mTORC1\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, constitutive targeting epistasis, widely replicated\",\n      \"pmids\": [\"20381137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Ragulator functions as a guanine nucleotide exchange factor (GEF) for RagA and RagB (RRAGB), stimulating GTP loading of these GTPases in response to amino acids in a v-ATPase-dependent fashion. Two additional Ragulator components (HBXIP and C7orf59) were identified as required for mTORC1 activation by amino acids.\",\n      \"method\": \"In vitro GEF assay, Co-immunoprecipitation, nucleotide loading assays, genetic knockdown\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro biochemical GEF activity assay plus cell-based validation, replicated\",\n      \"pmids\": [\"22980980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Glutaminolysis (conversion of glutamine to α-ketoglutarate) activates mTORC1 upstream of the Rag GTPases by promoting GTP loading of RagB and lysosomal translocation of mTORC1. Inhibition of glutaminolysis prevented RagB GTP loading; constitutively active Rag heterodimer rescued mTORC1 activation in absence of glutaminolysis, placing RagB downstream of α-ketoglutarate production.\",\n      \"method\": \"Nucleotide loading assays for RagB, epistasis with constitutively active Rag heterodimer, lysosomal translocation imaging\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct RagB GTP loading measured, constitutively active Rag epistasis, multiple methods\",\n      \"pmids\": [\"22749528\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Leucyl-tRNA synthetase (LRS) functions as a GAP (GTPase-activating protein) for Rag GTPases (including RagB/RRAGB) in response to intracellular leucine, binding directly to the Rag GTPase in an amino acid-dependent manner to activate mTORC1 signaling.\",\n      \"method\": \"In vitro GAP assay, Co-immunoprecipitation, mutagenesis of leucine-binding residues of LRS\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro GAP activity demonstrated, leucine-binding site mutagenesis, direct binding shown\",\n      \"pmids\": [\"22424946\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"p62/SQSTM1 binds the Rag GTPases (including RagB/RRAGB) in an amino acid-dependent manner, favors formation of the active Rag heterodimer stabilized by raptor, colocalizes with Rags at the lysosomal compartment, and is required for mTORC1 interaction with Rag GTPases and for mTORC1 translocation to the lysosome.\",\n      \"method\": \"Co-immunoprecipitation, co-localization imaging, amino acid-dependent interaction assays, knockdown with mTORC1 activation readouts\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, localization, and functional epistasis in multiple cell contexts\",\n      \"pmids\": [\"21981924\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"GATOR1 (composed of DEPDC5, Nprl2, Nprl3) has GTPase-activating protein (GAP) activity toward RagA and RagB (RRAGB), functioning as a negative regulator of Rag GTPases and hence mTORC1. Inactivating mutations in GATOR1 components in human cancers cause mTORC1 hyperactivation and amino acid insensitivity.\",\n      \"method\": \"In vitro GAP assay, cancer cell line GATOR1 knockdown, amino acid starvation epistasis, mutant analysis\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro GAP activity demonstrated for RagA/B, cancer mutation analysis, widely replicated\",\n      \"pmids\": [\"23723238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"RagC and RagD were identified as novel GTP-binding proteins that interact with RagA and RagB (RRAGB) via their C-terminal regions (containing a leucine zipper and coiled-coil structure). RagC/D associated with both GDP- and GTP-bound forms of RagA. RagC and RagD changed their subcellular localization depending on the nucleotide-bound state of RagA, establishing the RagA/B–RagC/D heterodimer paradigm.\",\n      \"method\": \"Yeast two-hybrid, GST pulldown, radiolabeled GTP/GDP binding assay, subcellular localization studies\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro GTP binding, pulldown, and localization studies; foundational discovery of Rag heterodimer\",\n      \"pmids\": [\"11073942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Folliculin (FLCN) is recruited to lysosomal surfaces upon amino acid depletion and directly binds RagA/B (including RRAGB) via its GTPase domain, and together with FNIP1 promotes amino acid-dependent mTORC1 recruitment to lysosomes via Rag GTPases.\",\n      \"method\": \"Co-immunoprecipitation, lysosomal localization imaging, amino acid starvation/stimulation assays, FLCN knockout/knockdown\",\n      \"journal\": \"Journal of Cell Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding to RagA/B demonstrated, lysosomal recruitment shown, functional epistasis\",\n      \"pmids\": [\"24081491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Sestrins bind the heterodimeric RagA/B–RagC/D GTPases and function as guanine nucleotide dissociation inhibitors (GDIs) for RagA/B (including RRAGB), inhibiting amino acid-induced Rag guanine nucleotide exchange and mTORC1 lysosomal translocation. A conserved GDI motif is required; its mutation creates dominant-negative Sestrin rendering mTORC1 insensitive to amino acid deprivation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro GDI assay, mutagenesis of GDI motif, cell-permeable peptide inhibition, mouse knockout\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro GDI activity demonstrated, GDI motif mutagenesis, mouse model validation\",\n      \"pmids\": [\"25259925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SLC38A9, a lysosomal transmembrane amino acid transporter, interacts with Rag GTPases (including RRAGB) and Ragulator in an amino acid-sensitive manner, transporting arginine with high Km. Loss of SLC38A9 represses mTORC1 activation by amino acids (particularly arginine); overexpression of its Ragulator-binding domain renders mTORC1 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, lysosomal localization imaging, loss-of-function and gain-of-function genetic epistasis\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — transport assay, direct interaction with Rag GTPases, epistasis upstream of Rags; replicated in parallel Nature paper\",\n      \"pmids\": [\"25567906\", \"25561175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SZT2 recruits a fraction of GATOR1 and GATOR2 to form a SZT2-orchestrated GATOR (SOG) complex essential for GATOR- and Sestrin-dependent nutrient sensing and mTORC1 regulation via Rag GTPases (including RRAGB). SZT2 deficiency causes constitutive mTORC1 signaling under nutrient deprivation; lysosomal localization of SOG is required for its function.\",\n      \"method\": \"Co-immunoprecipitation, lysosomal localization, genetic knockout mouse, epistasis with GATOR1/GATOR2 overexpression\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, mouse knockout, and functional epistasis; independent study\",\n      \"pmids\": [\"28199315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TRIM37 interacts with mTOR and RRAGB, enhances the mTOR–RRAGB interaction, and promotes lysosomal localization of mTOR, thereby activating amino acid-stimulated mTORC1 signaling. Loss of TRIM37 reduces TFEB phosphorylation, causing its nuclear translocation and transcriptional activation of lysosome biogenesis and autophagy genes.\",\n      \"method\": \"Co-immunoprecipitation, lysosomal localization imaging, TRIM37 knockdown/knockout, TFEB phosphorylation and nuclear translocation assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and localization with functional readouts; single lab study\",\n      \"pmids\": [\"29940807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NUFIP2 contributes to mTOR inactivation (via the Ragulator-RRAGA-RRAGB complex) together with LGALS8 (galectin-8) at the lysosome following lysosomal damage. GABARAPs interact directly with NUFIP2 and are required (via Atg8ylation) for NUFIP2 recruitment to damaged lysosomes, where it inhibits the Rag GTPase complex.\",\n      \"method\": \"Proteomic studies of damaged lysosomes, Co-immunoprecipitation, lysosome immunopurification (LysoIP), mTOR activity assays, GABARAP knockout\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — proteomics + Co-IP + functional mTOR readout; single lab study\",\n      \"pmids\": [\"36394332\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"circEXOC6B (a circular RNA) inhibits the heterodimer formation of RRAGB by directly binding to it, thereby suppressing mTORC1 pathway activity. HIF1A transcriptionally upregulates RRAGB by binding to its promoter, creating a HIF1A-RRAGB-mTORC1 positive feedback loop in colorectal cancer that circEXOC6B can interrupt.\",\n      \"method\": \"RNA pull-down, RNA-binding protein immunoprecipitation, Co-immunoprecipitation, chromatin immunoprecipitation, dual-luciferase assay, in vivo xenograft\",\n      \"journal\": \"Molecular Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple orthogonal RNA-protein interaction assays plus ChIP; single lab, circRNA context\",\n      \"pmids\": [\"35739524\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RRAGB overexpression in glioblastoma cells reduces proliferation, migration, and invasion and induces G0/G1 cell cycle arrest. RRAGB upregulation decreases expression of PI3K, phosphorylated AKT, mTOR, and S6K; restoring AKT activation rescues GBM cell proliferative and invasive properties, indicating RRAGB suppresses GBM progression partly through blockade of the PI3K/AKT signaling axis.\",\n      \"method\": \"RRAGB overexpression in GBM cell lines, western blot for PI3K/AKT/mTOR/S6K, AKT activator rescue experiment, xenograft and orthotopic mouse models\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — gain-of-function with pathway rescue experiment and in vivo validation; single lab\",\n      \"pmids\": [\"37517217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RRAGB is a target of miR-21-3p in endothelial progenitor cells (EPCs); overexpression of RRAGB activates the mTOR pathway, inhibits autophagic activity, and impairs EPC proliferation, migration, and tube formation. Berberine downregulates RRAGB through upregulation of miR-21-3p, restoring EPC function and promoting wound healing.\",\n      \"method\": \"Luciferase reporter assay (miR-21-3p/RRAGB targeting), RRAGB overexpression in EPCs, western blot for mTOR/autophagy markers, EPC functional assays, DVT mouse model\",\n      \"journal\": \"Regenerative Therapy\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, indirect (miRNA-mediated) RRAGB manipulation without direct biochemical characterization\",\n      \"pmids\": [\"39100534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CircMRP4 acts as a sponge for miR-499-5p, leading to upregulation of RRAGB and consequent activation of mTORC1/P70S6K signaling in podocytes under high glucose conditions, promoting podocyte apoptosis and inflammation in diabetic kidney disease.\",\n      \"method\": \"Dual-luciferase reporter, RNA immunoprecipitation, RNA pull-down, RRAGB expression/knockdown, mTORC1/P70S6K western blot, in vivo DKD mouse model\",\n      \"journal\": \"Cellular Signalling\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — indirect (circRNA/miRNA-mediated) manipulation of RRAGB; single lab\",\n      \"pmids\": [\"39842531\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RRAGB (RagB) is a Ras-family small GTPase that forms obligate heterodimers with RagC or RagD and functions as a central node in amino acid sensing to mTORC1: when GTP-loaded (stimulated by Ragulator acting as its GEF, leucyl-tRNA synthetase acting as a Rag GAP, and regulated by GATOR1 GAP activity and Sestrin GDI activity), the RagA/B–RagC/D heterodimer recruits mTORC1 to lysosomal membranes where it is activated by Rheb, while upstream sensors including SLC38A9 (arginine), glutaminolysis (α-ketoglutarate), FLCN, p62, NUFIP2, and TRIM37 modulate this process; RRAGB also suppresses PI3K/AKT signaling in certain tumor contexts and is subject to transcriptional regulation by HIF1A and post-transcriptional regulation by miRNAs.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RRAGB encodes a Ras-related GTPase that functions within the Ragulator–Rag heterodimer complex at the lysosomal surface to transduce amino acid and stress signals to mTORC1. TRIM37 enhances the MTOR–RRAGB interaction and promotes lysosomal mTOR recruitment, thereby activating mTORC1 and suppressing TFEB-driven autophagy/lysosome biogenesis [PMID:29940807], while the circular RNA circEXOC6B directly binds RRAGB and inhibits Rag heterodimer formation, disrupting a HIF1A–RRAGB–mTORC1 positive feedback loop in colorectal cancer [PMID:35739524]. Following lysosomal damage, NUFIP2 and galectin-8 engage the Ragulator–RRAGA–RRAGB complex to inactivate mTORC1 in a GABARAP-dependent manner [PMID:36394332]. RRAGB expression is also regulated by miR-21-3p and the circMRP4/miR-499-5p axis, and its overexpression activates mTORC1/P70S6K signaling in multiple cellular contexts while, paradoxically, suppressing PI3K/AKT/mTOR signaling and tumor growth in glioblastoma [PMID:37517217, PMID:39842531, PMID:39100534].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"TRIM37 was shown to bridge MTOR and RRAGB, establishing that an E3 ubiquitin ligase promotes the physical MTOR–RRAGB interaction required for lysosomal mTORC1 activation and downstream TFEB regulation.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, lysosomal localization assays, TFEB phosphorylation and translocation readouts upon TRIM37 siRNA knockdown in mammalian cells\",\n      \"pmids\": [\"29940807\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TRIM37 ubiquitinates RRAGB or MTOR directly to facilitate complex assembly is unknown\",\n        \"The nucleotide-loading state of RRAGB required for TRIM37 interaction was not defined\",\n        \"Whether other Rag GTPase heterodimer combinations (e.g., RRAGA–RRAGC) are similarly regulated by TRIM37 was not tested\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Two studies revealed that RRAGB-containing Rag complexes serve as a convergence node for both nutrient-driven signaling and lysosomal damage responses: circEXOC6B directly binds RRAGB to block heterodimer formation and suppress mTORC1/HIF1A signaling, while NUFIP2/galectin-8 engage the Ragulator–RRAGA–RRAGB complex after membrane damage to inactivate mTORC1.\",\n      \"evidence\": \"RNA pull-down, mass spectrometry, RIP, ChIP, and luciferase assays for circEXOC6B–RRAGB interaction (colorectal cancer cells); lysosome immunopurification proteomics, co-IP, and genetic knockdown with mTORC1 readouts for NUFIP2 recruitment (lysosomal damage model)\",\n      \"pmids\": [\"35739524\", \"36394332\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The structural basis of circEXOC6B binding to RRAGB and how it sterically prevents heterodimer formation is unresolved\",\n        \"Whether NUFIP2 contacts RRAGB directly or acts through other Ragulator subunits was not fully distinguished\",\n        \"Relative contributions of RRAGB versus RRAGC in the lysosomal damage-sensing pathway were not dissected\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"RRAGB overexpression was found to suppress glioblastoma cell growth by decreasing PI3K/AKT/mTOR/S6K signaling, revealing a context-dependent tumor-suppressive role that positions RRAGB upstream of PI3K in addition to its canonical role downstream of amino acids.\",\n      \"evidence\": \"Overexpression and knockdown in GBM cell lines with AKT-activator rescue, xenograft and orthotopic mouse tumor models\",\n      \"pmids\": [\"37517217\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The molecular mechanism by which RRAGB suppresses PI3K expression is unknown—whether direct or indirect\",\n        \"This tumor-suppressive effect contradicts the canonical mTORC1-activating role and has not been reconciled mechanistically\",\n        \"Findings are from a single laboratory and have not been independently replicated\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"miR-21-3p was validated as a direct post-transcriptional repressor of RRAGB, linking microRNA regulation to RRAGB-dependent mTORC1 activation and autophagy suppression in endothelial progenitor cells.\",\n      \"evidence\": \"Dual-luciferase reporter confirming miR-21-3p targeting of RRAGB 3′UTR, overexpression/knockdown functional assays in EPCs, DVT mouse model\",\n      \"pmids\": [\"39100534\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether miR-21-3p regulation of RRAGB is relevant outside the EPC/DVT context is untested\",\n        \"The GTP-loading state of RRAGB produced by this miRNA axis was not assessed\",\n        \"Single-laboratory finding without independent confirmation\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The circMRP4/miR-499-5p sponge axis was shown to upregulate RRAGB and activate mTORC1/P70S6K signaling, promoting podocyte apoptosis under diabetic conditions and extending RRAGB's pathological relevance to kidney disease.\",\n      \"evidence\": \"Dual-luciferase, RIP, RNA pull-down confirming circMRP4–miR-499-5p–RRAGB axis; knockdown/overexpression in podocytes under high glucose\",\n      \"pmids\": [\"39842531\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether RRAGB activation alone is sufficient for podocyte apoptosis or requires concurrent metabolic stress is unclear\",\n        \"Single-laboratory study in cell culture and limited in vivo validation\",\n        \"The specific Rag heterodimer partner (RRAGC vs RRAGD) in podocytes was not identified\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of RRAGB's GTPase cycle regulation, how RRAGB can paradoxically suppress PI3K/AKT in some tumor contexts while activating mTORC1 in others, and whether disease-associated RRAGB mutations alter Rag heterodimer function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No GEF or GAP specific to RRAGB has been identified in these studies\",\n        \"No structural data for RRAGB in the heterodimer or bound to circRNA exists\",\n        \"The context-dependent switch between mTORC1 activation and PI3K suppression lacks a mechanistic explanation\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 3, 4, 5]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"complexes\": [\n      \"Ragulator-Rag complex\"\n    ],\n    \"partners\": [\n      \"MTOR\",\n      \"TRIM37\",\n      \"RRAGA\",\n      \"NUFIP2\",\n      \"HIF1A\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"RRAGB (RagB) is a Ras-family small GTPase that forms obligate heterodimers with RagC or RagD and serves as a central mediator of amino acid signaling to mTORC1, coupling nutrient availability to cell growth [PMID:18497260, PMID:11073942]. In response to amino acids, RagB is loaded with GTP through the guanine nucleotide exchange activity of the lysosome-anchored Ragulator complex, while leucyl-tRNA synthetase and GATOR1 act as GAPs, and Sestrins function as GDIs to negatively regulate its activation; the active RagB–RagC/D heterodimer recruits mTORC1 to lysosomal membranes where it is activated by Rheb [PMID:22980980, PMID:22424946, PMID:23723238, PMID:25259925, PMID:20381137]. Upstream nutrient inputs including arginine sensing via the lysosomal transporter SLC38A9, glutaminolysis-derived α-ketoglutarate, folliculin (FLCN), p62/SQSTM1, and the SZT2-organized GATOR complex converge on the RagB nucleotide cycle to tune mTORC1 activation [PMID:25567906, PMID:22749528, PMID:24081491, PMID:21981924, PMID:28199315]. RRAGB overexpression in glioblastoma cells suppresses proliferation through inhibition of PI3K/AKT signaling, and HIF1A transcriptionally upregulates RRAGB, indicating additional regulatory and context-dependent roles in cancer biology [PMID:37517217, PMID:35739524].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Identification of RagC/D as obligate heterodimeric partners of RagA/B established the fundamental Rag GTPase architecture, resolving how these atypical small GTPases are organized.\",\n      \"evidence\": \"Yeast two-hybrid, GST pulldown, and GTP/GDP binding assays in mammalian cells\",\n      \"pmids\": [\"11073942\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No upstream regulation or downstream effector identified at this stage\", \"Functional relevance of heterodimer to signaling pathways unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Linking RagB GTP loading to amino acid-dependent mTORC1 activation and lysosomal translocation revealed the core physiological function of the Rag GTPases, answering what signal they relay and to whom.\",\n      \"evidence\": \"Co-IP of Rag–Raptor, constitutively active/dominant-negative RagB mutants, mTOR lysosomal localization imaging\",\n      \"pmids\": [\"18497260\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism anchoring Rag GTPases to lysosomes unknown\", \"Identity of the RagB GEF and GAP unresolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery that the Ragulator complex tethers Rag GTPases to lysosomes and that constitutive lysosomal targeting of mTORC1 bypasses Rag/Ragulator dependence established lysosomal recruitment as the rate-limiting step in amino acid sensing.\",\n      \"evidence\": \"Co-IP, lysosomal localization imaging, constitutively lysosome-targeted mTORC1 epistasis\",\n      \"pmids\": [\"20381137\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Ragulator has catalytic activity toward Rag GTPases undetermined\", \"Upstream amino acid sensors unidentified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identification of p62/SQSTM1 as an amino acid-dependent binding partner of Rag GTPases that stabilizes the active heterodimer and promotes mTORC1 lysosomal recruitment added a regulatory scaffold component to the pathway.\",\n      \"evidence\": \"Co-IP, co-localization imaging, amino acid-dependent interaction assays, knockdown with mTORC1 readouts\",\n      \"pmids\": [\"21981924\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise mechanism by which p62 stabilizes the active Rag configuration unclear\", \"Relationship to p62's role in autophagy not dissected\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Three concurrent discoveries defined the enzymology governing RagB nucleotide state: Ragulator as the GEF, leucyl-tRNA synthetase as a leucine-sensing GAP, and glutaminolysis/α-ketoglutarate as an upstream signal promoting RagB GTP loading.\",\n      \"evidence\": \"In vitro GEF assay for Ragulator, in vitro GAP assay for LRS with leucine-binding mutagenesis, RagB nucleotide loading assays with glutaminolysis inhibition and constitutively active Rag rescue\",\n      \"pmids\": [\"22980980\", \"22424946\", \"22749528\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of Ragulator GEF activity unresolved\", \"LRS GAP activity questioned by later studies regarding specificity for RagD vs RagB\", \"How α-ketoglutarate mechanistically influences RagB GTP loading unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identification of GATOR1 as a RagA/B GAP and FLCN as a direct RagA/B-binding protein defined key negative and positive regulators converging on Rag nucleotide cycling, and linked GATOR1 loss-of-function to cancer.\",\n      \"evidence\": \"In vitro GAP assay for GATOR1 on RagA/B, cancer cell line GATOR1 knockdown; Co-IP of FLCN with RagA/B, FLCN knockout epistasis\",\n      \"pmids\": [\"23723238\", \"24081491\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether FLCN has direct catalytic activity toward Rag GTPases unresolved at this point\", \"Structural basis of GATOR1 GAP mechanism unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstration that Sestrins act as GDIs for RagA/B revealed a distinct inhibitory mechanism—blocking nucleotide exchange rather than stimulating GTP hydrolysis—adding a new regulatory modality to the pathway.\",\n      \"evidence\": \"In vitro GDI assay, GDI motif mutagenesis, cell-permeable peptide inhibition, mouse knockout\",\n      \"pmids\": [\"25259925\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Sestrin GDI activity is itself regulated by stress signals incompletely understood\", \"Whether Sestrins have additional Rag-independent functions in mTORC1 regulation unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"SLC38A9 was identified as a lysosomal arginine sensor upstream of Rag GTPases, providing the first mechanistic link between a specific amino acid transporter and the Rag-mTORC1 pathway.\",\n      \"evidence\": \"Co-IP of SLC38A9 with Rag GTPases and Ragulator, arginine transport assay, loss-of-function and gain-of-function epistasis\",\n      \"pmids\": [\"25567906\", \"25561175\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SLC38A9 mechanistically alters Rag nucleotide state not determined\", \"Whether SLC38A9 senses luminal arginine directly or indirectly debated\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovery that SZT2 organizes GATOR1/GATOR2 into the SOG complex at lysosomes explained how GATOR-mediated Rag regulation is spatially coordinated, resolving how nutrient-insensitive mTORC1 signaling arises from SZT2 deficiency.\",\n      \"evidence\": \"Co-IP, lysosomal localization, genetic knockout mouse, GATOR1/2 epistasis\",\n      \"pmids\": [\"28199315\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SZT2 has additional scaffolding roles beyond GATOR complex organization unknown\", \"Structural basis of SOG complex assembly unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"TRIM37 was shown to enhance the mTOR–RRAGB interaction and promote mTOR lysosomal localization, identifying a new positive regulator that also connects Rag-mTORC1 signaling to TFEB-dependent lysosome biogenesis.\",\n      \"evidence\": \"Co-IP of TRIM37 with mTOR and RRAGB, lysosomal localization imaging, TFEB phosphorylation assays\",\n      \"pmids\": [\"29940807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether TRIM37's E3 ligase activity is required for its effect on RRAGB not established\", \"Single-lab finding awaiting independent replication\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Two studies expanded the regulatory landscape: NUFIP2/galectin-8 were found to inactivate the Rag complex at damaged lysosomes, and circEXOC6B was shown to directly bind RRAGB to inhibit heterodimer formation, while HIF1A was identified as a transcriptional activator of RRAGB.\",\n      \"evidence\": \"LysoIP proteomics, Co-IP, mTOR activity assays for NUFIP2; RNA pull-down, RIP, ChIP, dual-luciferase, xenograft for circEXOC6B/HIF1A\",\n      \"pmids\": [\"36394332\", \"35739524\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which NUFIP2 inhibits Rag nucleotide state not biochemically defined\", \"circEXOC6B binding site on RRAGB uncharacterized\", \"HIF1A–RRAGB transcriptional axis not validated outside colorectal cancer\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"RRAGB overexpression was shown to suppress glioblastoma cell proliferation via PI3K/AKT pathway inhibition, revealing a context-dependent tumor-suppressive function distinct from its canonical mTORC1-activating role.\",\n      \"evidence\": \"RRAGB overexpression in GBM cell lines, PI3K/AKT/mTOR/S6K western blot, AKT activator rescue, xenograft and orthotopic models\",\n      \"pmids\": [\"37517217\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which RRAGB suppresses PI3K/AKT unclear—may be indirect via mTORC1 negative feedback\", \"Not reconciled with RagB's canonical role in mTORC1 activation\", \"Single lab, single cancer type\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RRAGB's tumor-suppressive activity via PI3K/AKT inhibition is mechanistically reconciled with its canonical role in mTORC1 activation, and whether RRAGB mutations contribute to human Mendelian disease or are recurrently altered in cancer, remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of full-length human RagB–RagC/D heterodimer bound to effectors\", \"No direct disease-causing mutations in RRAGB reported\", \"Context-dependent pro- versus anti-proliferative roles not mechanistically resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 2, 3, 4, 6, 7, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 1, 2, 5, 8, 10, 11, 13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 6, 9, 10, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [12, 13]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3, 10, 11]}\n    ],\n    \"complexes\": [\n      \"Rag GTPase heterodimer (RagA/B–RagC/D)\",\n      \"Rag–Ragulator complex\"\n    ],\n    \"partners\": [\n      \"RRAGC\",\n      \"RRAGD\",\n      \"RPTOR\",\n      \"LAMTOR1\",\n      \"DEPDC5\",\n      \"FLCN\",\n      \"SQSTM1\",\n      \"SESN2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}