Affinage

RHOBTB3

Rho-related BTB domain-containing protein 3 · UniProt O94955

Length
611 aa
Mass
69.4 kDa
Annotated
2026-06-10
13 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RHOBTB3 is an atypical Rho-family ATPase that hydrolyzes ATP rather than GTP and acts as a Golgi- and endosome-associated organizer of membrane trafficking and substrate-targeted protein degradation (PMID:19490898). In its founding role it binds the Rab9 GTPase—which relieves RHOBTB3 autoinhibition to permit maximal ATP hydrolysis—and engages TIP47 on membranes to mediate cargo transport from endosomes to the trans-Golgi network, a function requiring both its N-terminal Rho-related domain and C-terminal Rab9-interaction sequences (PMID:19490898). RHOBTB3 also serves as a substrate-recognition scaffold for CUL3-RBX1 RING E3 ubiquitin ligase activity at the Golgi, ubiquitylating cyclin E to drive its degradation and enable normal S/G2 cell cycle progression; its loss arrests cells in S phase and fragments the Golgi (PMID:24145166). Beyond cyclin E, RHOBTB3 ubiquitinates AMBRA1 through K27-linked chains at K45 to promote its proteasomal degradation and thereby suppress autophagy (PMID:39404422), and it scaffolds a RHOBTB3/LIMD1–PHD2–VHL complex that promotes HIFα prolyl hydroxylation and ubiquitin-proteasomal degradation, restraining the Warburg effect and tumor growth (PMID:26215701, PMID:40311591). Its trafficking activities extend to assembly of a RHOBTB3–SHIP164–Vps26B complex at Golgi–early endosome contact sites that drives lipid-transfer-dependent endosome bud formation (PMID:38565878) and to maintenance of Golgi morphology and Golgi–ER carrier trafficking (PMID:32354068).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2009 High

    Established the biochemical identity of RhoBTB3 as an ATP-hydrolyzing (not GTP-hydrolyzing) Rho-family protein and placed it in endosome-to-TGN transport, answering what kind of enzyme it is and what regulates it.

    Evidence Direct binding and ATPase assays, co-IP, and domain-replacement genetics in cultured cells showing Rab9 binding relieves autoinhibition and TIP47 interaction on membranes

    PMID:19490898

    Open questions at the time
    • Structural basis of the autoinhibited-to-open transition not resolved
    • How ATP hydrolysis is coupled mechanically to cargo release at the Golgi not defined
  2. 2012 Medium

    Tested whether RhoBTB3's CUL3 association extends to all binding partners by examining the 5-HT7a serotonin receptor, showing it stabilizes the receptor without ubiquitinating it—revealing CUL3-independent functions.

    Evidence Yeast two-hybrid, co-IP, domain mapping, and proteasome-inhibition assays in HEK293T cells

    PMID:22245496

    Open questions at the time
    • Mechanism by which RhoBTB3 protects 5-HT7a from proteasomal degradation unknown
    • Physiological context of the interaction not established
  3. 2013 High

    Defined RhoBTB3 as the substrate-recognition subunit of a Golgi-localized CUL3-RBX1 E3 ligase targeting cyclin E, linking its trafficking compartment to cell cycle control.

    Evidence RNAi depletion, reciprocal co-IP, ubiquitylation assays, cell cycle analysis, and Golgi localization experiments

    PMID:24145166

    Open questions at the time
    • Why a Golgi-localized ligase targets a nuclear/cytoplasmic cyclin not mechanistically resolved
    • Whether ATPase activity is required for ligase function not established
  4. 2015 High

    Extended RhoBTB3 into oxygen sensing by showing it scaffolds PHD2 and VHL with LIMD1 to maximize HIFα hydroxylation and degradation, defining a tumor-suppressive metabolic role.

    Evidence Co-IP, hydroxylation and ubiquitination assays, RNAi knockdown, and xenograft experiments

    PMID:26215701

    Open questions at the time
    • How hypoxia disassembles the complex molecularly not defined
    • Relationship between this scaffolding role and ATPase activity unknown
  5. 2019 Medium

    Addressed the in vivo organismal function via knockout mice, revealing a role in platelet alpha-granule secretion and collagen-dependent thrombus formation distinct from its trafficking phenotypes.

    Evidence Knockout mouse model with flow cytometry, aggregometry, granule secretion assays, and collagen adhesion under flow

    PMID:30754723

    Open questions at the time
    • Molecular link between RhoBTB3 and granule secretion machinery not identified
    • Whether the platelet phenotype reflects trafficking or ligase functions unknown
  6. 2020 Medium

    Resolved RhoBTB3's direct presence on Golgi–ER carriers and its requirement for normal carrier trafficking and Golgi morphology, reinforcing a direct trafficking role at the Golgi interface.

    Evidence RNAi, high-content image-based screening, and live-cell imaging of carrier trafficking

    PMID:32354068

    Open questions at the time
    • Molecular cargo carried by these carriers not defined
    • Whether RhoBTB3 ATPase cycle drives carrier dynamics not tested
  7. 2024 Medium

    Identified a RHOBTB3–SHIP164–Vps26B complex at Golgi–early endosome contacts driving lipid-transfer-dependent endosome budding, and a separate E3 ligase activity toward AMBRA1 that suppresses autophagy.

    Evidence Co-IP, RNAi, fluorescence/live imaging, rescue with lipid-transfer-defective and K45 ubiquitination-site mutants, and IP-MS substrate identification

    PMID:38565878 PMID:39404422

    Open questions at the time
    • How RHOBTB3 coordinates contact-site scaffolding with bud formation not resolved
    • Whether the AMBRA1 ligase activity uses CUL3 not specified
    • Relationship between the trafficking and autophagy roles unknown
  8. 2025 Medium

    Corroborated the RhoBTB3–PHD2–HIF-1α axis in skin in vivo and showed it is pharmacologically targetable, with diosmetin reducing complex formation to stabilize HIF-1α.

    Evidence Co-IP, RNA-seq, rAAV overexpression in mice, immunohistochemistry, and a UV sunburn model

    PMID:40311591

    Open questions at the time
    • Direct binding site of diosmetin and whether it acts on RhoBTB3 or PHD2 not established
    • Tissue specificity of the skin phenotype not explained

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RhoBTB3's single ATPase scaffold protein selects among its diverse functions—endosome-TGN transport, CUL3 ligase activity toward distinct substrates, contact-site lipid-transfer scaffolding, and HIF degradation—remains unresolved.
  • No structural model integrating the ATPase cycle with substrate/partner selection
  • Determinants directing RhoBTB3 to one complex versus another not identified
  • Whether ATP hydrolysis is required across all of its roles untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 3 GO:0016874 ligase activity 2 GO:0060090 molecular adaptor activity 2 GO:0140657 ATP-dependent activity 1
Localization
GO:0005794 Golgi apparatus 3 GO:0005768 endosome 2 GO:0005783 endoplasmic reticulum 2 GO:0005886 plasma membrane 1
Pathway
R-HSA-392499 Metabolism of proteins 3 R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-1640170 Cell Cycle 1 R-HSA-8953897 Cellular responses to stimuli 1 R-HSA-9612973 Autophagy 1
Complex memberships
RHOBTB3/LIMD1–PHD2–VHL–HIFα complexRHOBTB3–CUL3–RBX1 E3 ubiquitin ligaseRHOBTB3–SHIP164–Vps26B complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 RhoBTB3 binds directly to Rab9 GTPase and functions with Rab9 in protein transport from endosomes to the trans-Golgi network. Biochemical analysis revealed that RhoBTB3 binds and hydrolyzes ATP (not GTP), and Rab9 binding opens the autoinhibited RhoBTB3 protein to permit maximal ATP hydrolysis. RhoBTB3 also interacts with TIP47 on membranes, suggesting a role in releasing this cargo selection protein from vesicles for efficient docking and fusion at the Golgi. Gene replacement experiments showed that both the N-terminal Rho-related domain and C-terminal sequences (important for Rab9 interaction) are required for function. Direct binding assays, biochemical ATPase activity assays, co-immunoprecipitation, gene replacement experiments in cultured cells Cell High 19490898
2013 RhoBTB3 is a Golgi-associated ATPase that targets cyclin E for ubiquitylation as part of a CUL3-dependent RING-E3 ubiquitin ligase complex (RhoBTB3–CUL3–RBX1) at the Golgi. Depletion of RhoBTB3 arrests cells in S phase, triggers Golgi fragmentation, and elevates cyclin E levels. Golgi association of the complex is required for its ability to catalyze cyclin E ubiquitylation and allow normal S/G2 cell cycle progression. RNAi depletion, co-immunoprecipitation, ubiquitylation assays, cell cycle analysis, Golgi localization experiments The Journal of cell biology High 24145166
2015 RHOBTB3 directly interacts with the prolyl hydroxylase PHD2 to promote HIFα hydroxylation, and directly interacts with VHL (an E3 ubiquitin ligase complex component) to facilitate HIFα ubiquitination. RHOBTB3 dimerizes with LIMD1 and assembles a RHOBTB3/LIMD1–PHD2–VHL–HIFα complex for maximal HIFα degradation. Hypoxia reduces this complex formation, causing HIFα accumulation. RHOBTB3 deficiency elevates the Warburg effect and accelerates xenograft tumor growth. Co-immunoprecipitation, ubiquitination assays, hydroxylation assays, RNAi knockdown, xenograft experiments Cell research High 26215701
2012 RhoBTB3 interacts with the 5-HT7a serotonin receptor (binding involves both the C-terminal tail and the third intracellular loop of the receptor), co-localizes at the plasma membrane and ER, and inhibits proteasomal degradation of the 5-HT7a receptor. Notably, although RhoBTB3 interacts with CUL3, it does not recruit CUL3/ROC1 to the 5-HT7a receptor and does not mediate receptor ubiquitination. Yeast two-hybrid screen, co-immunoprecipitation in HEK293T cells, domain mapping, immunofluorescence microscopy, proteasome inhibition assays Cellular signalling Medium 22245496
2020 Depletion of RhoBTB3 affects Golgi complex morphology and causes changes in the trafficking speeds of membrane carriers operating at the Golgi–ER interface. RhoBTB3 was found to be present on these Golgi–ER carriers, indicating a direct role in this trafficking step. RNA interference, high-content image-based screening, live-cell imaging of carrier trafficking, fluorescence microscopy Cells Medium 32354068
2024 RhoBTB3 forms a complex with SHIP164 and the retromer subunit Vps26B at Golgi–early endosome (EE) contact sites to promote EE bud formation. Vps26B acts as a novel Rab14 effector, and Rab14 activity regulates SHIP164 association with EEs. Suppression of RhoBTB3 phenocopies SHIP164 depletion (enlarged Rab14+ EEs without buds), revealing a lipid-transfer-dependent pathway for EE budding. Co-immunoprecipitation, RNAi knockdown, fluorescence microscopy, rescue experiments with lipid-transfer-defective mutants Cell discovery Medium 38565878
2024 RhoBTB3 negatively regulates autophagy by acting as an E3 ubiquitin ligase that ubiquitinates AMBRA1 (at K45 via K27-linked ubiquitin chains), promoting its proteasome-mediated degradation. RhoBTB3 deficiency induces autophagy and elevates AMBRA1 protein levels (without affecting AMBRA1 mRNA), while RhoBTB3 overexpression inhibits autophagy induction. AMBRA1 knockdown blocks RhoBTB3-depletion-induced autophagy. Immunoprecipitation, mass spectrometry, ubiquitination assays with site-specific mutants (K45), proteasome inhibition assays, RNAi knockdown, overexpression Cells Medium 39404422
2025 Diosmetin reduces formation of the RhoBTB3–PHD2 complex in UV-irradiated keratinocytes, thereby limiting HIF-1α hydroxylation and ubiquitination, and stabilizing HIF-1α. Overexpression of RhoBTB3 in mice enriches RhoBTB3, PHD2, and HIF-1α in the epidermis, consistent with RhoBTB3 promoting PHD2-mediated HIF-1α hydroxylation in skin. Co-immunoprecipitation, RNA sequencing, rAAV-mediated overexpression in mice, immunohistochemistry, in vivo UV sunburn model Phytomedicine Medium 40311591
2019 Genetic deletion of RhoBTB3 in mice leads to increased alpha-granule secretion in platelets in response to thrombin, CRP, and U46619/ADP, and reduces platelet accrual on collagen under flow conditions, without affecting platelet count, granule numbers, surface receptors, aggregation, dense granule secretion, or tail bleeding time. Knockout mouse model, flow cytometry, aggregometry, granule secretion assays, collagen adhesion under flow Cells Medium 30754723

Source papers

Stage 0 corpus · 13 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 RhoBTB3: a Rho GTPase-family ATPase required for endosome to Golgi transport. Cell 79 19490898
2015 RHOBTB3 promotes proteasomal degradation of HIFα through facilitating hydroxylation and suppresses the Warburg effect. Cell research 48 26215701
2013 Golgi-associated RhoBTB3 targets cyclin E for ubiquitylation and promotes cell cycle progression. The Journal of cell biology 39 24145166
2022 RhoBTB3 Regulates Proliferation and Invasion of Breast Cancer Cells via Col1a1. Molecules and cells 20 35698915
2012 RhoBTB3 interacts with the 5-HT7a receptor and inhibits its proteasomal degradation. Cellular signalling 15 22245496
2014 Expression analysis of mouse Rhobtb3 using a LacZ reporter and preliminary characterization of a knockout strain. Histochemistry and cell biology 10 24923387
2023 MicroRNA-142-3p promotes renal cell carcinoma progression by targeting RhoBTB3 to regulate HIF-1 signaling and GGT/GSH pathways. Scientific reports 9 37045834
2021 High Expression of RhoBTB3 Predicts Favorable Chemothrapy Outcomes in non-M3 Acute Myeloid Leukemia. Journal of Cancer 7 34093823
2020 RNA Interference Screening Identifies Novel Roles for RhoBTB1 and RhoBTB3 in Membrane Trafficking Events in Mammalian Cells. Cells 7 32354068
2024 Biogenesis of Rab14-positive endosome buds at Golgi-endosome contacts by the RhoBTB3-SHIP164-Vps26B complex. Cell discovery 5 38565878
2019 Alterations in Platelet Alpha-Granule Secretion and Adhesion on Collagen under Flow in Mice Lacking the Atypical Rho GTPase RhoBTB3. Cells 4 30754723
2024 RhoBTB3 Functions as a Novel Regulator of Autophagy by Suppressing AMBRA1 Stability. Cells 2 39404422
2025 Diosmetin attenuates the ubiquitination of epidermal hypoxia-inducible factor 1 alpha by diminishing the formation of RhoBTB3/PHD2 complex in ultraviolet radiation-induced sunburn in mice. Phytomedicine : international journal of phytotherapy and phytopharmacology 1 40311591

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