Affinage

RRAGA

Ras-related GTP-binding protein A · UniProt Q7L523

Length
313 aa
Mass
36.6 kDa
Annotated
2026-06-10
22 papers in source corpus 11 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RRAGA (RagA) is a Ras-related GTP-binding protein that functions as the master nutrient sensor controlling mTORC1 activation at the lysosome and broader TOR-dependent control of growth, autophagy, and aging (PMID:7499430, PMID:24768164). Biochemically it binds GTP in a specific, saturable, and rapidly exchangeable manner but lacks detectable intrinsic GTPase activity, defining a novel Ras-homologous subfamily with an unusually large C-terminal domain (PMID:7499430). In its GTP-loaded state RagA recruits mTORC1 to the lysosomal surface to enable amino-acid-dependent mTORC1 activation, and loss of RagA abolishes nutrient regulation of mTORC1 while leaving growth-factor sensitivity intact, causing embryonic lethality and growth defects in mice; RagA-dependent mTORC1 activity in turn suppresses PI3K/Akt signaling (PMID:24768164, PMID:31711501). Signaling is terminated by a negative feedback loop in which Skp2 catalyzes K63-linked ubiquitination of RagA to recruit the GATOR1 GAP complex, driving GTP hydrolysis and attenuating mTORC1 recruitment (PMID:26051179). The nucleotide-bound state also governs RagA's nucleocytoplasmic distribution, with dominant-negative RagA relocalizing to nuclear speckles co-localizing with SC-35 (PMID:9394008). Beyond mTORC1, RagA acts as the primary in vivo suppressor of TFEB nuclear translocation independently of mTORC1, links to the dynein motor through DYNLT binding at its G3 nucleotide-binding box (PMID:26227614), and promotes endolysosomal degradation of CD47 to enhance phagocytic clearance of cancer cells (PMID:36823443). A gain-of-function RRAGA missense mutation (p.Leu60Arg) causing autosomal dominant cataract drives increased lysosomal localization, mTORC1 hyperactivation, and suppressed autophagy in lens epithelial cells (PMID:27294265).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1995 High

    Established RagA as a biochemical entity: a Ras-related protein that binds and exchanges GTP but, unlike canonical GTPases, lacks intrinsic hydrolytic activity, predicting it would require an external GAP.

    Evidence GST-fusion radiolabeled GTPγS binding assays and sequence alignment with recombinant protein

    PMID:7499430

    Open questions at the time
    • No cellular function assigned at this stage
    • GAP and exchange factors unidentified
    • Role of the large C-terminal domain undefined
  2. 1998 High

    Linked RagA's nucleotide state to its subcellular distribution and placed it functionally in the Ran/Gsp1 GTPase pathway via yeast complementation, the first connection between RagA conformation and localization.

    Evidence Yeast complementation of gtr1-11, genetic suppressor analysis, and SC-35 co-localization imaging of T21L and Q66L mutants

    PMID:9394008

    Open questions at the time
    • Mammalian relevance of Ran-pathway link not demonstrated
    • mTORC1 role not yet known
    • Mechanism of nuclear speckle relocalization unexplained
  3. 2010 Medium

    Demonstrated in vivo that RagA orthologs act upstream in the TOR pathway to control lifespan and behavioral aging, tying nucleotide-state mutants to organismal physiology.

    Evidence C. elegans loss-, gain-, and dominant-negative genetics with RNAi epistasis and locomotion assays

    PMID:20523893

    Open questions at the time
    • Molecular mechanism downstream of TOR not dissected
    • Single model organism
    • Lysosomal recruitment mechanism not addressed
  4. 2014 High

    Defined RagA as essential and nutrient-specific for mammalian mTORC1 activation, separating amino-acid from growth-factor inputs and revealing feedback suppression of PI3K/Akt.

    Evidence Constitutive and tissue-specific mouse knockouts with mTORC1 and PI3K/Akt signaling readouts

    PMID:24768164

    Open questions at the time
    • How amino acid signals load GTP onto RagA not resolved
    • Mechanism of PI3K/Akt suppression unclear
  5. 2015 High

    Identified the negative-feedback circuit that turns RagA signaling off: Skp2-mediated K63 ubiquitination recruits the GATOR1 GAP to drive RagA-GTP hydrolysis, answering how the GTPase-activity-less RagA is inactivated.

    Evidence Reciprocal Co-IP, K63-linkage-specific ubiquitination assays, and mTORC1 lysosomal localization with autophagy/cell-size readouts

    PMID:26051179

    Open questions at the time
    • Stoichiometry and ubiquitination site mapping incomplete
    • Deubiquitinase counterbalance not identified
  6. 2015 Medium

    Mapped a direct physical link between RagA and the dynein motor, suggesting motor-based positioning of RagA via its nucleotide-binding region.

    Evidence NMR binding-residue mapping at the G3 box plus Co-IP/pulldown defining a tripartite complex with dynein intermediate chain

    PMID:26227614

    Open questions at the time
    • Functional consequence of dynein binding for mTORC1 signaling untested
    • Single lab, no in vivo validation
  7. 2016 Medium

    Provided a human disease link, showing a RRAGA gain-of-function mutation causes mTORC1 hyperactivation and autophagy suppression underlying autosomal dominant cataract.

    Evidence Functional assays in human lens epithelial cells: lysosomal imaging, mTORC1 phosphorylation, autophagy and growth assays

    PMID:27294265

    Open questions at the time
    • No in vitro reconstitution of mutant GTPase behavior
    • Single lab
  8. 2019 Low

    Extended the lysosomal recruitment role to inflammatory signaling and identified candidate upstream regulators acting through RagA.

    Evidence siRNA knockdown with mTORC1/p70S6K readouts (PC12 cells); Co-IP of WDR35/IFT121 with Rag-dependent S6 phosphorylation

    PMID:30570184 PMID:31711501

    Open questions at the time
    • WDR35 link rests on a single Co-IP without mechanistic dissection
    • Direct vs indirect WDR35-RagA interaction unresolved
  9. 2023 Medium

    Revealed an mTORC1-independent function of RagA in cargo turnover, driving endolysosomal degradation of CD47 to control phagocytic clearance.

    Evidence Co-IP, lysosomal localization and CD47 stability assays, RAGA loss-of-function and phagocytosis assays

    PMID:36823443

    Open questions at the time
    • Mechanism coupling RagA to CD47 endocytosis unclear
    • Whether GTP state controls CD47 degradation untested
  10. 2025 Medium

    Established Rag GTPases including RagA as the primary in vivo suppressors of TFEB, distinct from their mTORC1 role, with loss triggering renal cystogenesis.

    Evidence Conditional RagA/B mouse renal knockout with mTORC1, TFEB localization, and cystogenesis readouts (preprint)

    Open questions at the time
    • Preprint, not peer-reviewed
    • Direct biochemical basis of mTORC1-independent TFEB suppression undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • The molecular events that load GTP onto RagA in response to amino acids, and how a single GTPase coordinates its mTORC1-dependent and mTORC1-independent (TFEB, CD47) outputs, remain unresolved.
  • No identified amino-acid-responsive GEF for RagA in the corpus
  • Structural basis for selecting downstream effectors unknown
  • Integration of dynein-based positioning with signaling output untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060089 molecular transducer activity 2 GO:0098772 molecular function regulator activity 2 GO:0003924 GTPase activity 1
Localization
GO:0005764 lysosome 3 GO:0005654 nucleoplasm 1 GO:0005829 cytosol 1
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-9612973 Autophagy 2 R-HSA-168256 Immune System 1
Partners
CD47DYNLT1GATOR1MTORSKP2WDR35
Complex memberships
Rag GTPase complex

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 RagA (and RagBs) are novel Ras-related GTP-binding proteins that bind GTP in a specific and saturable manner; bound GTP is rapidly exchangeable but no intrinsic GTPase activity was detected. They share ~52% identity with yeast Gtr1p, defining a novel subfamily of Ras-homologous GTPases with an unusually large C-terminal domain. GST fusion protein GTP-binding assay (radiolabeled GTPγS), sequence alignment, recombinant protein biochemistry The Journal of biological chemistry High 7499430
1998 RagA is a functional homologue of S. cerevisiae Gtr1p and participates in the Ran/Gsp1-GTPase pathway: human RagA and RagBs rescued cold sensitivity of gtr1-11 yeast, and a dominant-negative RagA (T21L) partially suppressed both rcc1- and rna1-1 mutations. Wild-type RagA localizes to the cytoplasm, but the dominant-negative T21L form relocalizes to nuclear speckles co-localizing with SC-35, while constitutively active Q66L remains cytoplasmic — indicating nucleotide-state-dependent nucleocytoplasmic shuttling. Yeast complementation assay, genetic epistasis (suppressor analysis), fluorescence localization/immunostaining with SC-35 co-localization Journal of cell science High 9394008
2010 In C. elegans, raga-1 (RagA ortholog) acts in the TOR pathway to regulate lifespan and behavioral aging: loss-of-function extended vigorous locomotion late in life; gain-of-function curtailed behavioral vitality and shortened lifespan; dominant-negative lengthened lifespan. RNAi experiments placed raga-1 upstream in the TOR pathway. C. elegans genetics (loss-of-function, gain-of-function, dominant-negative mutants), RNAi epistasis, behavioral assays (locomotion frequency) PLoS genetics Medium 20523893
2014 RagA is essential for embryonic development and for mTORC1 activation by nutrients in mammals: RagA-null mouse embryos die at E10.5 with loss of mTORC1 activity, severe growth defects, and abrogation of nutrient regulation of mTORC1, while growth-factor sensitivity of mTORC1 is maintained. Deletion of RagA in adult mice is also lethal. RagA-specific deletion in liver increases PI3K/Akt signaling, establishing that RagA-dependent mTORC1 activity normally suppresses PI3K/Akt. Conditional and constitutive mouse knockout (RagA and RagB), primary cell mTORC1 activity assays (nutrient and growth factor stimulation), genetic epistasis Developmental cell High 24768164
2015 Skp2 E3 ligase mediates K63-linked ubiquitination of RagA; this ubiquitination facilitates recruitment of the GATOR1 complex (a GAP for RagA) to RagA, promoting GTP hydrolysis and thereby attenuating mTORC1 lysosomal recruitment and activation. This constitutes a negative feedback loop activated by amino acids in an mTORC1-dependent manner to prevent mTORC1 hyperactivation. Co-immunoprecipitation, ubiquitination assays (K63-linkage specificity), mTORC1 lysosomal localization assay, loss-of-function and overexpression with downstream signaling readouts (autophagy, cell size, cilia growth) Molecular cell High 26051179
2015 DYNLT (Tctex-1 dynein light chain) interacts with RagA via a β-strand in RagA's G3 box (nucleotide-binding region), forming a tripartite complex with dynein intermediate chain, thereby linking RagA to the dynein motor. Both microtubule-associated and cytoplasmic DYNLT can bind RagA equally. NMR spectroscopy mapping of binding residues, Co-IP/pulldown, identification of interacting domain by deletion mapping The FEBS journal Medium 26227614
2016 RRAGA missense mutations (p.Leu60Arg) associated with autosomal dominant cataracts cause increased relocalization of RRAGA to lysosomes, up-regulated mTORC1 phosphorylation, down-regulated autophagy, and altered cell growth in human lens epithelial cells, mechanistically linking RRAGA gain-of-function to mTORC1 hyperactivation and cataract pathology. Functional studies in human lens epithelial cells: lysosomal localization imaging, mTORC1 phosphorylation assays, autophagy assays, cell growth assays, promoter activity assays PLoS genetics Medium 27294265
2019 RagA is required for mTORC1 translocation to lysosomal membranes: siRNA silencing of RagA in PC12 cells blocked LPS-induced mTORC1 lysosomal translocation and activation of p70S6K. siRNA knockdown, immunofluorescence for mTORC1 lysosomal co-localization, Western blot for p70S6K phosphorylation Journal of neuroinflammation Medium 31711501
2019 RagA interacts with WDR35/IFT121 (a hedgehog signaling/ciliary protein); overexpression of WDR35 decreases phosphorylation of ribosomal S6 protein in a RagA-, RagB-, and RagC-dependent manner, suggesting WDR35 is an upstream negative regulator of mTORC1 acting through RagA. Co-immunoprecipitation, overexpression with S6 phosphorylation readout, genetic dependence (RagA/B/C requirement) Genes to cells Low 30570184
2023 RAGA (RagA) interacts with CD47 and promotes CD47 lysosomal localization and degradation via the endocytosis/lysosome pathway; disruption of RAGA blocks CD47 degradation, leading to CD47 accumulation and increased plasma membrane CD47 expression, thereby reducing phagocytic clearance of cancer cells. Co-immunoprecipitation, lysosomal localization assay, RAGA loss-of-function, phagocytosis assay, CD47 protein stability assay Communications biology Medium 36823443
2023 In Drosophila gut, RagA knockdown alone induces intestinal thickening and foregastric enlargement. RagA knockdown rescues intestinal thinning and decreased secretory cells in nprl2 mutants (genetic epistasis placing RagA downstream of Nprl2 for these phenotypes), but does not rescue the enlarged forestomach of nprl2 mutants, indicating Nprl2 regulates forestomach development through a RagA-independent mechanism. Drosophila genetics (RagA RNAi knockdown, nprl2 mutants, double mutant epistasis), immunofluorescence for intestinal morphology and cell composition Sheng wu gong cheng xue bao = Chinese journal of biotechnology Medium 37154336
2024 Hyperactivation of mTORC1 regulator RAGA-1 in C. elegans preserved ribosomal proteins during starvation and accelerated growth recovery after short starvation, but reduced survival under prolonged starvation, demonstrating that RAGA-1-dependent mTORC1 activity controls autophagy-dependent ribosomal protein turnover and balances starvation survival versus recovery speed. Live imaging, proteomics (proteome quantification), C. elegans RAGA-1 gain-of-function genetics, starvation survival assays bioRxivpreprint Medium
2025 In renal tubular epithelial cells, RagA/B deletion inhibits mTORC1 but triggers renal cystogenesis driven by TFEB nuclear translocation; Rag GTPases (including RagA) suppress TFEB in vivo independently of mTORC1, establishing that Rag GTPases are the primary suppressors of TFEB in this context rather than acting solely through mTORC1. Conditional RagA/B knockout in mouse renal tubular epithelial cells, mTORC1 activity assays, TFEB nuclear localization assays, cystogenesis phenotype, genetic epistasis bioRxivpreprint Medium

Source papers

Stage 0 corpus · 22 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1995 Cloning of a novel family of mammalian GTP-binding proteins (RagA, RagBs, RagB1) with remote similarity to the Ras-related GTPases. The Journal of biological chemistry 110 7499430
2014 RagA, but not RagB, is essential for embryonic development and adult mice. Developmental cell 81 24768164
1998 RagA is a functional homologue of S. cerevisiae Gtr1p involved in the Ran/Gsp1-GTPase pathway. Journal of cell science 80 9394008
2015 Skp2-Mediated RagA Ubiquitination Elicits a Negative Feedback to Prevent Amino-Acid-Dependent mTORC1 Hyperactivation by Recruiting GATOR1. Molecular cell 76 26051179
2010 Manipulation of behavioral decline in Caenorhabditis elegans with the Rag GTPase raga-1. PLoS genetics 73 20523893
2007 Characterization of RagA and RagB in Porphyromonas gingivalis: study using gene-deletion mutants. Journal of medical microbiology 71 17965357
1997 RAGA: RNA sequence alignment by genetic algorithm. Nucleic acids research 45 9358168
2016 Mutations of RagA GTPase in mTORC1 Pathway Are Associated with Autosomal Dominant Cataracts. PLoS genetics 29 27294265
2019 Potential link between the RagA-mTOR-p70S6K axis and depressive-behaviors during bacterial liposaccharide challenge. Journal of neuroinflammation 14 31711501
2021 The RagA and RagB proteins of Porphyromonas gingivalis. Molecular oral microbiology 13 34032024
2021 Botanical Drug Puerarin Ameliorates Liposaccharide-Induced Depressive Behaviors in Mice via Inhibiting RagA/mTOR/p70S6K Pathways. Oxidative medicine and cellular longevity 11 34707778
2015 DYNLT (Tctex-1) forms a tripartite complex with dynein intermediate chain and RagA, hence linking this small GTPase to the dynein motor. The FEBS journal 11 26227614
2023 RAGA prevents tumor immune evasion of LUAD by promoting CD47 lysosome degradation. Communications biology 9 36823443
2016 A morphological and molecular study of Pseudocorynosoma Aznar, Pérez Ponce de León and Raga 2006 (Acanthocephala: Polymorphidae) from Mexico with the description of a new species and the presence of cox 1 pseudogenes. Parasitology international 9 27865888
2024 Brain Specific RagA Overexpression Triggers Depressive-Like Behaviors in Mice via Activating ADORA2A Signaling Pathway. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 8 39373701
2009 The FIP-1 like polyadenylation factor in trypanosomes and the structural basis for its interaction with CPSF30. Biochemical and biophysical research communications 8 19338765
2021 Clinical significance of ragA, ragB, and PG0982 genes in Porphyromonas gingivalis isolates from periodontitis patients. European journal of oral sciences 7 33667038
2019 RagA, an mTORC1 activator, interacts with a hedgehog signaling protein, WDR35/IFT121. Genes to cells : devoted to molecular & cellular mechanisms 6 30570184
2025 The FIP 1.0 Data Set: Highly resolved annotated image time series of 4,000 wheat plots grown in 6 years. GigaScience 4 40498535
2022 Generation of a RRAGA knockout human iPSC line GIBHi002-A-5 using CRISPR/Cas9 technology. Stem cell research 3 35870248
2023 [The regulatory relationship between RagA and Nprl2 in Drosophila gut development]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology 1 37154336
2025 Hyperactivation of mTORC1 by an endogenous raga-1 gain-of-function mutation does not reduce lifespan in C. elegans. microPublication biology 0 40385374

Missed literature

Know a paper Affinage missed for RRAGA? Flag it for the maintainers and the community.

No submissions yet.