Affinage

VPS39

Vam6/Vps39-like protein · UniProt Q96JC1

Length
886 aa
Mass
101.8 kDa
Annotated
2026-06-11
25 papers in source corpus 15 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

VPS39 is a membrane-tethering and trafficking scaffold that operates at the heart of endolysosomal sorting, organelle contact-site biology, and nutrient-sensing signaling (PMID:9111041, PMID:19748353, PMID:19748348). It was first defined in yeast as a subunit of a large vacuolar-membrane protein complex, where it physically associates with Vam2/Vps41 and is required for vacuolar protein sorting and vacuole biogenesis (PMID:9111041). Beyond tethering, yeast Vps39 acts as a guanine nucleotide exchange factor for the Rag-family GTPase Gtr1, loading it with GTP to activate the EGO complex and thereby stimulate TORC1 in response to amino acids, placing Vps39 upstream of Gtr1/Gtr2 → TORC1 in a conserved growth-control cascade (PMID:19748353, PMID:19748348, PMID:22344254). In mammalian cells VPS39 retains its lysosomal tethering role as a HOPS subunit but does not function as a Rab7 GEF, and a human isoform instead binds Rab5-GTP as a Rab5 effector (PMID:20363736, PMID:25750764). VPS39 additionally functions at mitochondria-lysosome membrane contact sites, where its recruitment supports phospholipid transfer—mitochondrial phosphatidylethanolamine accumulation in yeast and BMP biosynthesis and lysosomal cholesterol egress in mammalian cells—and maintains mitochondrial network integrity and basal autophagic flux (PMID:32058032, PMID:35452878, PMID:39605369). Through control of autophagy it negatively regulates ciliogenesis by governing IFT20 localization, and in iNKT cells it nucleates a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to negatively regulate mTORC1 (PMID:32077937, PMID:36741382). VPS39 loss impairs autophagic flux, alters insulin signaling and myoblast differentiation, and reduces skeletal muscle glucose uptake, and the gene is non-redundantly essential for early mouse embryonic development (PMID:33893273, PMID:20961651). Viral proteins from ASFV and SARS-CoV-2 hijack VPS39 to disrupt HOPS association and endolysosomal trafficking (PMID:36722971, PMID:39605369).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 1997 High

    Established VPS39 as a physical component of a vacuolar-membrane tethering complex, answering whether it acts at vacuoles and with which partner.

    Evidence Chemical cross-linking, co-sedimentation, GFP localization, and vacuolar protein-sorting assays in yeast

    PMID:9111041

    Open questions at the time
    • Stoichiometry and architecture of the complex not resolved
    • Did not address signaling or non-tethering roles
  2. 2009 High

    Revealed an unexpected enzymatic function beyond tethering—VPS39/Vam6 as a GEF for Gtr1 that activates TORC1 in response to amino acids.

    Evidence Genetic epistasis, dominant Gtr1 mutants, Co-IP, and TORC1 activity assays under amino-acid deprivation in budding yeast

    PMID:19748348 PMID:19748353

    Open questions at the time
    • Whether the GEF role is conserved in mammals not tested here
    • Structural basis of Gtr1 nucleotide exchange unresolved
  3. 2010 Medium

    Showed mammalian VPS39 diverges from its yeast counterpart by not acting as a Rab7 GEF, redefining its mammalian role at lysosomes.

    Evidence RILP-Rab7 effector pull-down, overexpression and dominant-negative VPS39, lysosomal morphology and growth-factor withdrawal assays

    PMID:20363736

    Open questions at the time
    • Mechanism of lysosomal clustering not defined
    • Identity of the relevant mammalian GTPase regulator left open
  4. 2010 Medium

    Demonstrated VPS39 is non-redundantly required for early mammalian development.

    Evidence Genetic knockout mouse with embryonic lethality analysis

    PMID:20961651

    Open questions at the time
    • Cellular cause of E6.5 lethality not determined
    • No conditional/tissue-specific dissection of essential function
  5. 2012 Medium

    Confirmed the Vam6 → Gtr1/Gtr2 → TORC1 cascade is conserved across yeasts, supporting a deeply conserved nutrient-sensing role.

    Evidence Genetic epistasis and Gtr1/Gtr2-TORC1 co-localization in fission yeast

    PMID:22344254

    Open questions at the time
    • Direct biochemical GEF activity not re-demonstrated in this system
    • Mammalian conservation still untested
  6. 2014 Medium

    Identified a human VPS39 isoform as a Rab5 effector, proposing it as a CORVET subunit and showing functional divergence from yeast.

    Evidence In vitro Rab5-GTP pull-down, co-localization in yeast and HEK293, and failed yeast complementation

    PMID:25750764

    Open questions at the time
    • Composition of a human CORVET complex not biochemically reconstituted
    • Functional consequence of Rab5 binding in cells not defined
  7. 2020 Medium

    Uncovered a HOPS/vCLAMP-independent moonlighting role for VPS39 in mitochondrial phosphatidylethanolamine accumulation, linking it to interorganelle lipid transfer.

    Evidence Lipid mass spectrometry, VPS39 vs HOPS/vCLAMP deletions, and PE-dependent fractionation in yeast

    PMID:32058032

    Open questions at the time
    • Molecular mechanism of PE transfer not resolved
    • Whether VPS39 carries lipid directly or recruits transfer machinery unknown
  8. 2020 Medium

    Connected VPS39 to negative control of ciliogenesis through autophagy-dependent regulation of IFT20.

    Evidence VPS39 knockdown in human renal cells, IFT20 localization and ciliogenesis imaging, and in vivo medaka model

    PMID:32077937

    Open questions at the time
    • Direct link between HOPS tethering and IFT20 turnover not established
    • Whether effect is cell-type specific unclear
  9. 2020 Medium

    Tested the predicted VPS39 C-terminal RING zinc finger, finding it does not adopt the expected fold under the conditions used.

    Evidence Recombinant expression, purification, and X-ray crystallography

    PMID:32724865

    Open questions at the time
    • Non-native fold attributed to His-tag and disulphide; native structure unresolved
    • Functional role of this domain unknown
  10. 2021 Medium

    Linked VPS39 deficiency to impaired autophagy, altered insulin signaling, epigenetic dysregulation, and reduced muscle glucose uptake, implicating it in metabolic disease.

    Evidence VPS39 siRNA in human myoblasts, autophagic flux and DNA methylation assays, and Vps39+/- mouse muscle glucose uptake

    PMID:33893273

    Open questions at the time
    • Causal chain from autophagy defect to epigenetic change not dissected
    • Direct VPS39 effector for insulin signaling not identified
  11. 2022 Medium

    Established VPS39 recruitment to mitochondria as a regulator of mitochondria-lysosome contact sites controlling mitochondrial network and autophagic flux.

    Evidence Cross-species transcriptomics/proteomics, fractionation and imaging of mitochondrial VPS39, and siRNA knockdown with morphology/flux assays

    PMID:35452878

    Open questions at the time
    • Trigger for SGPL1-driven recruitment mechanism incompletely defined
    • Direct tethering partners at the contact site not mapped
  12. 2023 Medium

    Showed ASFV CP204L sequesters VPS39 away from HOPS to reprogram endolysosomal trafficking for viral replication.

    Evidence Co-IP, co-localization, and VPS39 knockdown viral replication assays

    PMID:36722971

    Open questions at the time
    • Binding interface on VPS39 not mapped
    • Reciprocal validation of HOPS displacement limited
  13. 2023 Medium

    Defined a Rab7a-Vam6-AMPK complex through which VPS39 recruits AMPK to lysosomes to negatively regulate mTORC1, with VDAC1 as an antagonist.

    Evidence Co-IP of the ternary complex, Vam6 knockout mice, flow cytometry for mTORC1 activity, and lysosomal AMPK imaging in iNKT cells

    PMID:36741382

    Open questions at the time
    • Direct binding topology within the ternary complex not resolved
    • Generality beyond iNKT cells untested
  14. 2025 Medium

    Connected VPS39 to lysosomal cholesterol egress via NPC2/retromer trafficking and BMP biosynthesis, and identified SARS-CoV-2 ORF3a as a hijacker of this function.

    Evidence Co-IP, lipidomics, proteomics, and retromer/VPS39 deletion with cholesterol trafficking and MCS imaging (preprint)

    PMID:39605369

    Open questions at the time
    • Not yet peer-reviewed
    • Direct vs indirect role in NPC2 sorting not fully separated

Open questions

Synthesis pass · forward-looking unresolved questions
  • Whether mammalian VPS39 possesses any GEF/effector enzymatic activity analogous to its yeast Gtr1 role, and how a single scaffold coordinates HOPS tethering, contact-site lipid transfer, and nutrient signaling, remains unresolved.
  • No demonstrated mammalian GEF substrate
  • Structural basis for partitioning between distinct complexes unknown
  • How the same protein switches between vacuolar/lysosomal, mitochondrial, and signaling roles undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0005764 lysosome 3 GO:0005739 mitochondrion 2 GO:0005768 endosome 2 GO:0005773 vacuole 1
Pathway
R-HSA-9612973 Autophagy 3 R-HSA-162582 Signal Transduction 2 R-HSA-5653656 Vesicle-mediated transport 2
Partners
AMPKGTR1RAB5RAB7AVDAC1VPS41
Complex memberships
EGO complex (EGOC)HOPS complexRab7a-Vam6-AMPK complexvCLAMP

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1997 Vam6p/Vps39p physically interacts with Vam2p/Vps41p and both are components of a large protein complex on vacuolar membranes; loss of either protein results in defective vacuolar protein sorting (CPY, proteinase A, proteinase B, alkaline phosphatase) and accumulation of small vacuole-related structures. Vam6p-GFP localizes to specific regions of vacuolar membranes. Chemical cross-linking, co-sedimentation in detergent-resistant fractions, GFP tagging/fluorescence microscopy, subcellular fractionation, genetic deletion with vacuolar protein processing assays The Journal of biological chemistry High 9111041
2009 Yeast Vam6/Vps39 functions as a guanine nucleotide exchange factor (GEF) for the Rag GTPase homolog Gtr1, loading it with GTP to activate the EGO complex (EGOC) and thereby stimulate TORC1 in response to amino acids. Constitutively GTP-bound Gtr1 interacted strongly with TORC1 and conferred partial resistance to leucine deprivation; GDP-bound Gtr1 caused constitutively low TORC1 activity. Genetic epistasis, dominant active/inactive Gtr1 mutants, co-immunoprecipitation (Gtr1-TORC1 interaction), TORC1 activity assays under amino-acid deprivation Molecular cell High 19748348 19748353
2010 Mammalian Vps39 (mVps39) induces lysosomal clustering but does NOT increase Rab7-GTP levels when overexpressed, and a dominant-negative mVps39 mutant fragments lysosomes and promotes growth-factor independence without decreasing Rab7-GTP. These data indicate mVps39 is NOT a Rab7 GEF in mammalian cells. Effector pull-down assay (RILP-Rab7 GTP binding), overexpression and dominant-negative mVps39, lysosomal morphology imaging, growth-factor withdrawal survival assay The Journal of biological chemistry Medium 20363736
2012 In fission yeast, Vam6 functions upstream of Gtr1-Gtr2 and upstream of TORC1 in the amino-acid-sensing pathway; epistasis analyses placed Vam6 → Gtr1/Gtr2 → TORC1 in a conserved signaling cascade controlling cell growth and sexual differentiation. Genetic epistasis (deletion mutants combined with constitutively active/inactive Gtr alleles), co-localization of Gtr1/Gtr2 with TORC1 at vacuoles Journal of cell science Medium 22344254
2014 Human Vps39 isoform hVps39-2/TRAP1 co-localizes with Rab5 and directly binds Rab5-GTP in vitro, identifying it as a Rab5 effector and suggesting it is the missing Vps3 subunit of a putative human CORVET complex. Neither human Vps39 isoform could complement loss of yeast Vps39. In vitro pull-down with Rab5-GTP, co-localization by fluorescence microscopy in yeast and HEK293 cells, yeast complementation assay Cellular logistics Medium 25750764
2020 Yeast Vps39 is required specifically for ethanolamine-stimulated elevation of mitochondrial phosphatidylethanolamine (PE). Deletion of VPS39 prevented mitochondrial PE accumulation without affecting ER PE biosynthesis or transport to other organelles. Vps39 abundance and its recruitment to mitochondria and ER are dependent on local PE levels. This function is independent of the HOPS and vCLAMP complexes, representing a distinct moonlighting role. Lipid mass spectrometry, genetic deletion of VPS39 vs. HOPS/vCLAMP subunits, subcellular fractionation to assess Vps39 recruitment to mitochondria/ER under varying PE conditions Biochimica et biophysica acta. Molecular and cell biology of lipids Medium 32058032
2020 VPS39 (as a HOPS complex subunit) acts as a negative regulator of ciliogenesis in human renal cells by controlling the localization of IFT20 at the base of cilia through autophagy. This was confirmed in vivo in medaka fish renal tubules. VPS39 knockdown in human renal cells, IFT20 localization assay, ciliogenesis imaging, autophagy modulation, in vivo medaka fish model Human molecular genetics Medium 32077937
2021 VPS39 deficiency in human myoblasts impairs autophagic flux, alters insulin signaling, disrupts epigenetic enzyme activity and DNA methylation of myogenic regulators, and perturbs myoblast differentiation. Heterozygous Vps39+/- mice show reduced skeletal muscle glucose uptake. These effects mirror changes in myoblasts from individuals with type 2 diabetes. VPS39 siRNA knockdown in human myoblasts, autophagic flux assays, DNA methylation profiling, gene expression analysis, Vps39+/- mouse muscle glucose uptake assay Nature communications Medium 33893273
2022 SGPL1 upregulation stimulates VPS39 recruitment to mitochondria, enhancing mitochondria-lysosome membrane contact sites (MCS). VPS39 downregulation compromises mitochondrial network maintenance and basal autophagic flux in MICU1-deficient mammalian cells. In mouse-derived muscles, VPS39 recruitment to mitochondria is a signature of altered OXPHOS. Transcriptomics and proteomics in C. elegans micu-1 mutants, biochemical fractionation and imaging for VPS39 mitochondrial localization, VPS39 siRNA knockdown with mitochondrial morphology and autophagy flux assays in mammalian cells, mouse muscle tissue analysis Molecular metabolism Medium 35452878
2023 ASFV protein CP204L interacts with VPS39, blocking VPS39's association with the lysosomal HOPS complex, which modulates endolysosomal trafficking and promotes lysosome clustering. CP204L and VPS39 are redirected to virus factories. Loss of VPS39 reduces early-phase viral protein synthesis and delays ASFV replication. Co-immunoprecipitation, co-localization imaging, VPS39 knockdown with viral replication assays, HOPS complex assembly assays Journal of virology Medium 36722971
2023 Vam6/VPS39 in iNKT cells is essential for formation of a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to activate it; AMPK then negatively regulates mTORC1. VDAC1 inhibits this complex formation at mitochondria-lysosome contact sites, and Vam6 relieves this inhibition. Co-immunoprecipitation (Rab7a-Vam6-AMPK complex), flow cytometry for mTORC1 activity, genetic Vam6 knockout mice, imaging of lysosomal AMPK recruitment, RNA sequencing Frontiers in immunology Medium 36741382
2020 Crystal structure of the C-terminal proposed zinc-finger domain of VPS39 was solved, but it adopts a non-native fold (anti-parallel β-hairpin incorporated into a homotetrameric β-barrel stabilized by His-tag-coordinated zinc and an intramolecular disulphide), indicating this region does not form the predicted RING zinc finger under the purification conditions used. Recombinant protein expression, purification, X-ray crystallography Wellcome open research Medium 32724865
2025 VPS39 regulates NPC2 trafficking (via CI-MPR/retromer) and BMP biosynthesis to control lysosomal cholesterol egress. SARS-CoV-2 ORF3a binds VPS39, trapping CI-MPR and retromer in endosomes/lysosomes to impair NPC2 delivery and reducing lysosome-mitochondrion MCS, which decreases mitochondrial phosphatidylglycerol transfer needed for BMP synthesis. VPS39 deletion recapitulates both defects. Co-IP (ORF3a-VPS39 interaction), lipidomics (BMP and PG levels), proteomics, retromer/VPS39 deletion with cholesterol trafficking assays, MCS quantification by imaging bioRxivpreprint Medium 39605369
2010 VPS39-deficient mice die before embryonic day E6.5, demonstrating that VPS39 is non-redundantly essential for early embryonic development. Heterozygous mice show no overt phenotype. Genetic knockout mouse generation, embryonic lethality analysis Immunobiology Medium 20961651

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 The Vam6 GEF controls TORC1 by activating the EGO complex. Molecular cell 361 19748353
1997 Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the vacuolar membranes and involved in the vacuolar assembly in the yeast Saccharomyces cerevisiae. The Journal of biological chemistry 144 9111041
2010 Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence. The Journal of biological chemistry 102 20363736
2012 The Vam6 and Gtr1-Gtr2 pathway activates TORC1 in response to amino acids in fission yeast. Journal of cell science 54 22344254
2007 The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles. Development (Cambridge, England) 47 18077594
2021 VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. Nature communications 33 33893273
2010 The TGF-β signaling modulators TRAP1/TGFBRAP1 and VPS39/Vam6/TLP are essential for early embryonic development. Immunobiology 32 20961651
2014 The Vps39-like TRAP1 is an effector of Rab5 and likely the missing Vps3 subunit of human CORVET. Cellular logistics 25 25750764
2020 The HOPS complex subunit VPS39 controls ciliogenesis through autophagy. Human molecular genetics 20 32077937
2023 CP204L Is a Multifunctional Protein of African Swine Fever Virus That Interacts with the VPS39 Subunit of the Homotypic Fusion and Vacuole Protein Sorting Complex and Promotes Lysosome Clustering. Journal of virology 16 36722971
2020 Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine. Biochimica et biophysica acta. Molecular and cell biology of lipids 15 32058032
2021 Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 Is Involved in Maintenance of Mitochondrial and Vacuolar Functions under Oxidative Stress in Candida albicans. Antioxidants (Basel, Switzerland) 13 33478009
2009 Amino acid signaling to TOR activation: Vam6 functioning as a Gtr1 GEF. Molecular cell 13 19748348
2022 SGPL1 stimulates VPS39 recruitment to the mitochondria in MICU1 deficient cells. Molecular metabolism 10 35452878
2021 The Vacuolar Morphogenesis Protein Vam6-Like Protein Vlp1 Is Required for Pathogenicity of Cryptococcus neoformans. Journal of fungi (Basel, Switzerland) 9 34072011
2021 The Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 is Crucial for Autophagy in Candida albicans. Mycopathologia 8 34057669
2023 Vam6 reduces iNKT cell function in tumor via modulating AMPK/mTOR pathways. Frontiers in immunology 7 36741382
2021 Vam6/Vps39/TRAP1-domain proteins influence vacuolar morphology, iron acquisition and virulence in Cryptococcus neoformans. Cellular microbiology 7 34800311
2023 Role of VPS39, a key tethering protein for endolysosomal trafficking and mitochondria-lysosome crosstalk, in health and disease. Journal of cellular biochemistry 6 36924104
2025 SARS-CoV-2 ORF3a blocks lysosomal cholesterol egress by disrupting VPS39-regulated NPC2 trafficking and BMP metabolism. bioRxiv : the preprint server for biology 3 39605369
2020 Non-native fold of the putative VPS39 zinc finger domain. Wellcome open research 1 32724865
2026 Correction: Mao et al. Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 Is Involved in Maintenance of Mitochondrial and Vacuolar Functions Under Oxidative Stress in Candida albicans. Antioxidants 2021, 10, 136. Antioxidants (Basel, Switzerland) 0 41897552
2025 The HOPS and vCLAMP protein Vam6 connects polyphosphate with mitochondrial function and oxidative stress resistance in Cryptococcus neoformans. mBio 0 39998208
2025 Regulation of vacuole fusion in stomata by dephosphorylation of the HOPS subunit VPS39. The Plant journal : for cell and molecular biology 0 41418320
2024 Insights into the Role of VPS39 and Its Interaction with CP204L and A137R in ASFV Infection. Viruses 0 39339953

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