Affinage

AMBRA1

Activating molecule in BECN1-regulated autophagy protein 1 · UniProt Q9C0C7

Length
1298 aa
Mass
142.5 kDa
Annotated
2026-06-09
100 papers in source corpus 36 papers cited in narrative 33 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 9/9 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

AMBRA1 is a WD40-domain scaffold protein that couples autophagy initiation to cell-cycle control, signaling, and cell-fate decisions (PMID:17589504, PMID:33854235, PMID:33854239, PMID:33854232). In its founding role it positively regulates BECLIN1-dependent autophagy, and its loss in mouse embryos impairs autophagic flux and produces neural tube defects with unbalanced proliferation and apoptosis (PMID:17589504). Mechanistically, the BECLIN1-VPS34 complex is held inactive at the dynein motor through AMBRA1's interaction with dynein light chains; ULK1-mediated phosphorylation releases AMBRA1, allowing relocalization to the endoplasmic reticulum and mitochondria-associated membranes for autophagosome nucleation (PMID:20921139, PMID:21079415, PMID:33034545). AMBRA1 sits within a dense network of E3 ligases and kinases that tune its abundance and activity: it directs TRAF6-dependent K63 ubiquitylation of ULK1 in a positive feedback loop opposed by mTOR phosphorylation, while its own levels are restrained by Cullin-4 and RNF2/WASH-mediated K48 ubiquitylation and reset by USP7 deubiquitylation at K83/K86 (PMID:23524951, PMID:25499913, PMID:24980959, PMID:39887666). Independently of autophagosome formation, AMBRA1 serves as the substrate receptor of a CRL4 (CUL4-DDB1) ubiquitin ligase that drives proteasomal degradation of all three D-type cyclins, thereby restraining the G1-to-S transition and limiting replication stress; a 3.08 Å cryo-EM structure shows its N-terminal helix-loop-helix and WD40 domains clamping the DDB1 double-propeller to build the substrate-recruitment platform (PMID:33854235, PMID:33854239, PMID:33854232, PMID:37993427). As a CRL4 receptor AMBRA1 also ubiquitylates Elongin C and Smad4, linking it to CRL5 cross-regulation and TGFβ-driven EMT (PMID:30166453, PMID:34362797). In mitochondrial quality control, AMBRA1 drives both PINK1/PARKIN-dependent and -independent mitophagy, acting through PINK1/ATAD3A to stabilize PINK1 and through HUWE1/IKKα-mediated phosphorylation at S1014 to engage LC3/GABARAP (PMID:21753002, PMID:21921694, PMID:30217973, PMID:34798798, PMID:35593053). Through PP2A it promotes dephosphorylation and degradation of c-Myc, establishing AMBRA1 as a haploinsufficient tumor suppressor (PMID:25438055). Additional autophagy-independent functions include NF-κB/IKK regulation via the PP4R1/PP4c phosphatase complex and mitotic spindle orientation through CDK1/PLK1 phosphorylation and NUMA1 (PMID:38424148, PMID:37584777).

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 2007 High

    Established AMBRA1 as a positive regulator of autophagy and an essential developmental gene, answering whether it acts in the BECLIN1 pathway and what its loss does in vivo.

    Evidence RNAi and overexpression in vitro plus mouse knockout with phenotypic analysis

    PMID:17589504

    Open questions at the time
    • Did not define the molecular trigger linking AMBRA1 to autophagosome nucleation
    • Mechanism of the neural tube/proliferation phenotype unresolved
  2. 2010 High

    Resolved how AMBRA1 is held inactive and activated, showing dynein tethering of BECLIN1-VPS34 is released by ULK1 phosphorylation to permit ER relocalization.

    Evidence Co-IP, live-cell imaging, ULK1 kinase assays and DLC1-binding-site mutagenesis

    PMID:20921139 PMID:21079415

    Open questions at the time
    • Precise ER docking partners not identified at this stage
    • ULK1 phosphosites on AMBRA1 not fully mapped
  3. 2011 High

    Placed AMBRA1 within mitochondrial autophagy control through BCL-2 inhibition and Parkin-dependent recruitment to depolarized mitochondria, connecting it to mitophagy.

    Evidence Reciprocal Co-IP, fractionation, TAP-MS and endogenous Co-IP across HEK293, SH-SY5Y and mouse brain with knockdown readouts

    PMID:21358617 PMID:21753002 PMID:21921694

    Open questions at the time
    • Direct AMBRA1-driven steps in mitophagosome formation not biochemically reconstituted
    • BCL-2 binding interface not mapped at this point
  4. 2012 High

    Showed AMBRA1 is dismantled during apoptosis, defining a caspase/calpain switch (D482) that couples autophagy shutdown to cell death rate.

    Evidence In vitro cleavage assays, inhibitor treatment, D482 mutagenesis and cell death assays

    PMID:22441670

    Open questions at the time
    • Physiological contexts where this cleavage dominates unclear
    • Fate of cleavage fragments not yet characterized (addressed later)
  5. 2013 High

    Defined the kinase/ligase feedback architecture: mTOR inhibits AMBRA1, while dephosphorylated AMBRA1 recruits TRAF6 to K63-ubiquitylate and stabilize ULK1, with ULK1 reciprocally activating AMBRA1.

    Evidence Co-IP, K63-linkage-specific ubiquitylation assays, phospho-mapping and mTOR inhibition

    PMID:23524951

    Open questions at the time
    • mTOR target residues on AMBRA1 not exhaustively defined
    • Stoichiometry of the feedback loop not quantified
  6. 2014 High

    Identified the ubiquitin machinery controlling AMBRA1 abundance (Cullin-4, RNF2/WASH at K45) and a proliferation-restraining role via PP2A-mediated c-Myc degradation, establishing tumor-suppressor function.

    Evidence Reciprocal Co-IP, in vitro ubiquitination with linkage/site mapping, PP2A activity assays and mouse tumor models

    PMID:24980959 PMID:25438055 PMID:25499913

    Open questions at the time
    • How multiple ligases are coordinated temporally not resolved
    • Direct enzymatic basis of AMBRA1-stimulated PP2A activity unclear
  7. 2016 Medium

    Showed the caspase-generated AMBRA1 C-terminal fragment carries a BH3-like domain that binds and inhibits BCL-2, defining a proapoptotic feedback role for the cleavage product.

    Evidence Co-IP of AMBRA1-CT with BCL-2 and BH3-domain mutagenesis with apoptosis assays

    PMID:27123694

    Open questions at the time
    • Single-lab finding without reconstituted structural confirmation
    • Contribution relative to canonical BH3 proteins not quantified
  8. 2017 Medium

    Linked AMBRA1 to focal-adhesion signaling and to α-synuclein clearance, broadening its roles beyond canonical autophagy into Src/FAK trafficking and neurodegeneration-relevant cargo recognition.

    Evidence AP-MS interactomics, Co-IP, live imaging and invasion assays; phospho-S129 α-synuclein binding affinity assays with neuronal knockdown and MSA tissue

    PMID:27875637 PMID:28362576

    Open questions at the time
    • Direct vs scaffold-mediated nature of FAK/Src interactions not fully dissected
    • Structural basis of phospho-α-synuclein preference unknown
  9. 2018 High

    Defined a PINK1/PARKIN-independent mitophagy route (HUWE1/IKKα phosphorylating AMBRA1-S1014 to engage LC3/GABARAP) and immune/Treg functions via PP2A-FOXO3-FOXP3.

    Evidence In vitro IKKα kinase assay, S1014 phospho-mutant, LC3 interaction and mitophagy assays; Treg Co-IP and in vivo mouse models

    PMID:30217973 PMID:30513302

    Open questions at the time
    • Structural change induced by S1014 phosphorylation inferred, not resolved
    • Interplay between PINK1-dependent and -independent routes not reconciled
  10. 2019 Medium

    Refined mitophagy regulation (GSK-3β/MCL-1 gating of HUWE1 recruitment) and revealed a muscle TRIM32-ULK1 axis, connecting AMBRA1 to disease-linked autophagy in skeletal muscle.

    Evidence Co-IP, GSK-3β kinase assays, phospho-mutants, HUWE1 knockdown, ULK1 activity assays and TRIM32 disease-mutation tests

    PMID:31234693 PMID:31434979

    Open questions at the time
    • Single-lab mechanisms not independently reconstituted
    • Tissue specificity of these regulatory arms unclear
  11. 2020 Medium

    Localized AMBRA1's nucleation function to MAM raft-like microdomains via ERLIN1, GD3 and MFN2, defining the ER membrane platform for starvation-induced autophagosome formation.

    Evidence Co-IP, FRET, MAM fractionation and ERLIN1/ST8SIA1/MFN2 knockdowns

    PMID:33034545

    Open questions at the time
    • Direct vs lipid-dependent nature of the ERLIN1 interaction not separated
    • Single-lab without structural validation
  12. 2021 High

    Established the major autophagy-independent identity of AMBRA1 as the CRL4 substrate receptor degrading D-type cyclins, controlling G1/S and replication stress, and extended this receptor role to ELOC, Smad4 and ALDH1B1 substrates.

    Evidence Reconstituted in vitro ubiquitination, genome-wide CRISPR screens, mouse genetic models, DNA fiber/CHK1 synthetic-lethality assays, and substrate-specific ubiquitination/Co-IP assays

    PMID:30166453 PMID:33854232 PMID:33854235 PMID:33854239 PMID:34362797 PMID:34769507

    Open questions at the time
    • How substrate selection among cyclins, ELOC and Smad4 is regulated unknown
    • Crosstalk between CRL4-receptor and autophagy roles not integrated
  13. 2021 Medium

    Detailed AMBRA1's PINK1/ATAD3A mitophagy axis and disease-context roles in melanoma (FAK1) and medulloblastoma (SOCS3/STAT3), linking its loss to tumor aggressiveness.

    Evidence Co-IP, ATAD3A epistasis, LONP1-dependent PINK1 degradation assays; in vivo melanoma and medulloblastoma models with pathway inhibition

    PMID:33953176 PMID:34302498 PMID:34798798

    Open questions at the time
    • Direct biochemical basis of SOCS3 suppression not established
    • Whether FAK1 hyperactivation is direct or indirect not resolved
  14. 2022 High

    Demonstrated muscle-specific mitophagy dependence and a MAVS-stabilizing antiviral apoptosis role, separating AMBRA1's mitophagic and innate-immune functions.

    Evidence Muscle-specific conditional knockout with mitochondrial/respiratory phenotyping and mito-targeted rescue; AMBRA1-MAVS Co-IP, knockout and viral infection apoptosis assays

    PMID:34859815 PMID:35593053

    Open questions at the time
    • Selectivity of muscle mitophagy versus bulk autophagy mechanism unclear
    • MAVS stabilization mechanism (ligase competition) not defined
  15. 2023 High

    Provided the structural basis for CRL4 substrate recruitment (cryo-EM AMBRA1-DDB1) and a mitotic function (CDK1/PLK1 phosphorylation controlling NUMA1-dependent spindle orientation).

    Evidence 3.08 Å cryo-EM, HDX-MS, DDB1-binding mutagenesis and reconstituted ubiquitination; mitotic phospho-mapping, CDK1/PLK1 assays and spindle orientation assays

    PMID:37584777 PMID:37993427

    Open questions at the time
    • Substrate-engaging surface of the WD40 domain not resolved with cyclin bound
    • How mitotic phosphorylation reroutes AMBRA1 to NUMA1 not mechanistically detailed
  16. 2024 High

    Defined autophagy-independent NF-κB inflammation control via PP4R1/PP4c antagonism and an IKKα-S1043/CUL4A stabilization switch, plus BAG2-mediated localization control of AMBRA1.

    Evidence Co-IP, F1-domain/S1043 mutagenesis, IKKα kinase and CUL4A ubiquitination assays, conditional knockout mice; ULK1-complex interactomics with BAG2-S31A phospho-mutant

    PMID:38424148 PMID:39207901

    Open questions at the time
    • Integration of S1014 vs S1043 phosphorylation signals not resolved
    • Whether BAG2 sequestration competes with dynein tethering unknown
  17. 2025 Medium

    Identified a pro-oxidative function in intestinal epithelium where AMBRA1 antagonizes DUB3-mediated NRF2 deubiquitination, with USP7 stabilizing AMBRA1 at K83/K86 under oxidative stress.

    Evidence Co-IP, F1-domain and K83/K86 mutagenesis, in vitro deubiquitination, conditional knockout mice and IBD tissue analysis

    PMID:39887666

    Open questions at the time
    • Single-lab study without independent confirmation
    • Relationship between USP7-AMBRA1 stabilization and the CRL4 receptor pool unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How AMBRA1's distinct functions—autophagy scaffold, CRL4 substrate receptor, phosphatase regulator, and mitotic/spindle factor—are partitioned and switched within a cell remains unresolved.
  • No unified model of how post-translational marks route AMBRA1 between its competing complexes
  • Substrate-binding surface of the WD40 domain not structurally defined with a bound substrate
  • Quantitative partitioning of cytosolic, ER, and mitochondrial AMBRA1 pools unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0060090 molecular adaptor activity 4 GO:0098772 molecular function regulator activity 4
Localization
GO:0005739 mitochondrion 5 GO:0005783 endoplasmic reticulum 3 GO:0005634 nucleus 2 GO:0005856 cytoskeleton 1
Pathway
R-HSA-1640170 Cell Cycle 4 R-HSA-392499 Metabolism of proteins 4 R-HSA-9612973 Autophagy 4 R-HSA-162582 Signal Transduction 3 R-HSA-5357801 Programmed Cell Death 3
Partners
BECLIN1DDB1DLC1HUWE1PINK1PP2ATRAF6ULK1
Complex memberships
BECLIN1-VPS34 (class III PI3K) complexCRL4 (CUL4-DDB1) E3 ubiquitin ligaseULK1 complex

Evidence

Reading pass · 33 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 AMBRA1 is a positive regulator of BECLIN1-dependent autophagy; it bears a WD40 domain and interacts with BECLIN1 to promote autophagosome formation. Loss of AMBRA1 function in mouse embryos impairs autophagy, causes accumulation of ubiquitinated proteins, and leads to severe neural tube defects with unbalanced cell proliferation and excessive apoptosis. RNA interference in vitro, overexpression assays, mouse genetic knockout model with phenotypic analysis Nature High 17589504
2010 Under basal conditions, the BECLIN1-VPS34 complex is tethered to the dynein motor complex via AMBRA1's direct interaction with dynein light chains DLC1/2. Upon autophagy induction, ULK1 phosphorylates AMBRA1, releasing it from dynein; the complex then relocalizes to the endoplasmic reticulum, enabling autophagosome nucleation. Co-immunoprecipitation, live-cell imaging, ULK1 kinase assays, DLC1 knockdown, AMBRA1 DLC1-binding site mutagenesis The Journal of cell biology High 20921139 21079415
2011 Mitochondrial BCL-2 binds AMBRA1 and inhibits AMBRA1-induced autophagy. AMBRA1 preferentially binds the mitochondrial pool of BCL-2; upon autophagy induction this interaction is disrupted and AMBRA1 is recruited to BECLIN1. AMBRA1 can compete with both mitochondrial and ER-resident BCL-2 for BECLIN1 binding. Co-immunoprecipitation, subcellular fractionation, overexpression and knockdown assays The EMBO journal Medium 21358617
2011 Parkin interacts with AMBRA1 (identified by tandem affinity purification/mass spectrometry from HEK293 cells and validated by endogenous Co-IP). Upon prolonged mitochondrial depolarization, the Parkin–AMBRA1 interaction increases; AMBRA1 is recruited to perinuclear clusters of depolarized mitochondria in a Parkin-dependent manner and activates class III PI3K locally, promoting mitophagic clearance. Tandem affinity purification, mass spectrometry, endogenous Co-immunoprecipitation from HEK293, SH-SY5Y cells and adult mouse brain, siRNA knockdown, fluorescence microscopy The Journal of neuroscience High 21753002 21921694
2012 During apoptosis, AMBRA1 is proteolytically degraded by the combined action of caspases (cleaving at D482) and calpains (mediating complete degradation), dismantling autophagic activity. AMBRA1 levels are critical for the rate of apoptosis: RNAi-mediated knockdown sensitizes cells to apoptotic stimuli, while a caspase-non-cleavable AMBRA1 mutant prolongs autophagy and counteracts cell death. In vitro cleavage assays, caspase/calpain inhibitor treatment, site-directed mutagenesis (D482 site), RNA interference, cell death assays Cell death and differentiation High 22441670
2013 Under non-autophagic conditions, mTOR phosphorylates and inhibits AMBRA1. Upon autophagy induction, AMBRA1 is dephosphorylated and interacts with the E3 ligase TRAF6, supporting K63-linked ubiquitylation of ULK1, thereby stabilizing ULK1, promoting its self-association and function. ULK1 in turn activates AMBRA1 by phosphorylation, forming a positive feedback loop. Co-immunoprecipitation, ubiquitylation assays (K63-linkage specific), phosphorylation mapping, autophagy flux assays, mTOR inhibition experiments Nature cell biology High 23524951
2014 AMBRA1 regulates cell proliferation by facilitating dephosphorylation and degradation of c-Myc: AMBRA1 directly interacts with the phosphatase PP2A and enhances PP2A activity on c-Myc when mTOR is inhibited, reducing the cell division rate. AMBRA1-defective systems show deregulated c-Myc and increased tumorigenesis, establishing AMBRA1 as a haploinsufficient tumor suppressor. Co-immunoprecipitation (AMBRA1–PP2A interaction), PP2A phosphatase activity assay on c-Myc substrate, cell proliferation assays, mouse tumor models Nature cell biology High 25438055
2014 Cullin-4 E3 ubiquitin ligase binds AMBRA1 under basal conditions, limiting AMBRA1 protein abundance. Autophagy stimuli cause ULK1-dependent Cullin-4 release, stabilizing AMBRA1. Re-establishment of Cullin-4/AMBRA1 interaction later triggers AMBRA1 degradation, terminating autophagy. Upon Cullin-4 dissociation, AMBRA1 binds and inhibits Cullin-5, promoting DEPTOR accumulation and mTOR inhibition as a positive feedback loop. Co-immunoprecipitation, protein stability assays, autophagy flux measurement, ULK1 kinase-dependent dissociation assays Developmental cell High 25499913
2014 RNF2 associates with AMBRA1 as a K48-linked ubiquitin E3 ligase, ubiquitinating AMBRA1 at lysine 45 and targeting it for proteasomal degradation. WASH protein recruits RNF2 to AMBRA1; WASH deficiency impairs RNF2–AMBRA1 association and AMBRA1 degradation, thereby upregulating autophagy. Co-immunoprecipitation, in vitro ubiquitination assay with ubiquitin linkage mapping (K48), site-directed mutagenesis (K45), RNAi knockdown of RNF2 and WASH Cell research High 24980959
2016 The C-terminal fragment of AMBRA1 generated by caspase cleavage contains a BH3-like domain that directly binds and inhibits the antiapoptotic factor BCL-2, acting in a proapoptotic positive feedback loop during mitochondrial apoptosis. Co-immunoprecipitation of AMBRA1-CT with BCL-2, BH3 domain mutagenesis, apoptosis assays Autophagy Medium 27123694
2017 AMBRA1 acts as a 'spatial rheostat' controlling Src/FAK signaling: it binds both FAK and Src in cancer cells, recruits active phospho-Src away from focal adhesions into autophagic structures, and regulates cancer cell invasion. When FAK is present, AMBRA1 is recruited to focal adhesions, promoting FAK-dependent direction-sensing. Dynactin-1 and IFITM3 were identified as AMBRA1 binding partners mediating this trafficking function. Interaction proteomics (affinity purification-MS), Co-immunoprecipitation, live-cell imaging, AMBRA1 knockdown/rescue in squamous cell carcinoma cells, invasion assays eLife Medium 28362576
2018 AMBRA1 controls regulatory T cell (Treg) differentiation by interacting with PP2A phosphatase, promoting FOXO3 stability, which triggers FOXP3 transcription. AMBRA1 regulates Treg induction in vivo in tumor and multiple sclerosis mouse models. Co-immunoprecipitation (AMBRA1–PP2A), FOXO3 stability assays, AMBRA1 knockdown in T cells, in vivo mouse models Developmental cell Medium 30513302
2018 HUWE1 E3 ubiquitin ligase is a key inducer of AMBRA1-mediated, PINK1/PARKIN-independent mitophagy. HUWE1 activity enables IKKα to phosphorylate AMBRA1 at serine 1014, inducing structural changes in AMBRA1 that promote its interaction with LC3/GABARAP proteins and activate mitophagy. Co-immunoprecipitation, in vitro kinase assay (IKKα on AMBRA1-S1014), AMBRA1 phospho-mutant analysis, LC3 interaction assays, mitophagy flux assays Nature communications High 30217973
2018 HPV-E7 protein interacts with AMBRA1 and competes with its binding to BECLIN1, triggering calpain-dependent AMBRA1 degradation, thereby reducing autophagy activity in HPV-positive oropharyngeal squamous cell carcinoma cells. Co-immunoprecipitation, calpain inhibitor assays, competition binding experiments, autophagy flux assays Autophagy Medium 33172332
2019 MCL-1 inhibits AMBRA1-mediated mitophagy by blocking recruitment of HUWE1 E3 ligase to mitochondria. During AMBRA1-mediated mitophagy, GSK-3β phosphorylates MCL1 at S159, leading to HUWE1-dependent MCL1 degradation. GSK-3β inhibition sustains MCL1 levels and delays mitophagy. Co-immunoprecipitation, GSK-3β kinase assay, MCL1 phospho-mutant (S159A), HUWE1 knockdown, mitophagy flux assays Cell death and differentiation Medium 31434979
2019 TRIM32 E3 ubiquitin ligase is conveyed to ULK1 by AMBRA1 in muscle cells, stimulating ULK1 kinase activity through unanchored K63-linked polyubiquitin chains to induce autophagy upon atrophy. Limb-girdle muscular dystrophy 2H mutations in TRIM32 disrupt its ability to bind ULK1 and to induce autophagy. Co-immunoprecipitation, ULK1 kinase activity assay, ubiquitin linkage analysis, TRIM32 disease-mutation functional assays in muscle cells Autophagy Medium 31234693
2020 AMBRA1 interacts with ERLIN1 at mitochondria-associated membrane (MAM) raft-like microdomains, and this interaction is required for autophagosome formation upon nutrient starvation. The interaction depends on ganglioside GD3 and MFN2 integrity; knockdown of ERLIN1, ST8SIA1, or MFN2 impairs AMBRA1–ERLIN1 interaction and autophagy. Co-immunoprecipitation, FRET microscopy, subcellular fractionation to MAMs, ERLIN1/GD3-synthase/MFN2 knockdown, autophagy flux assays Autophagy Medium 33034545
2021 AMBRA1 serves as the substrate receptor for the CUL4-RING E3 ubiquitin ligase complex (CRL4AMBRA1/CRL4DCAF3) that ubiquitylates all three D-type cyclins (D1, D2, D3) for proteasomal degradation. Loss of AMBRA1 leads to cyclin D accumulation, RB hyperphosphorylation, and hyperproliferation. Cancer hotspot mutations in D-type cyclins abrogate their binding to AMBRA1 and stabilize them. Biochemical reconstitution of ubiquitylation, genome-wide CRISPR-Cas9 screen, Co-immunoprecipitation, mouse genetic models, in vitro ubiquitination assay, cancer mutation binding assays Nature High 33854232 33854235 33854239
2021 AMBRA1 regulates the G1-to-S phase transition and prevents replication stress by mediating proteasomal degradation of D-type cyclins and by controlling MYC/MYCN-mediated transcription of cyclin genes. AMBRA1-deficient cells show replication stress and CHK1 kinase dependency as a synthetic lethal vulnerability. Cyclin D stability assays, cell cycle analysis, DNA fiber assays (replication stress), CHK1 inhibitor synthetic lethality screen, in vivo neural stem cell and mouse models Nature High 33854232
2021 Upon mitochondrial depolarization, AMBRA1 is recruited to the outer mitochondrial membrane and interacts with PINK1 and ATAD3A (a transmembrane protein mediating PINK1 import and degradation). AMBRA1 deficiency reduces PINK1 stability by enhancing its degradation via the mitochondrial protease LONP1, decreasing PINK1-mediated ubiquitin phosphorylation and PARKIN recruitment. ATAD3A silencing rescues defective PINK1 accumulation in AMBRA1-deficient cells. Co-immunoprecipitation (AMBRA1–PINK1, AMBRA1–ATAD3A), AMBRA1 knockdown/ATAD3A knockdown epistasis, LONP1-dependent PINK1 degradation assays, mitophagy flux assays Autophagy High 34798798
2021 AMBRA1 (as the CRL4 substrate receptor) targets Elongin C (ELOC), the shared adapter of CRL5 ubiquitin ligase complexes, for polyubiquitination and degradation, thereby attenuating CRL5SOCS3 and CRL5VIF ligase activity. This cross-regulation modulates IL-6/STAT3 signaling and HIV-1 infectivity. Proteomics (affinity purification-MS), in vitro ubiquitination assay, Co-immunoprecipitation, CRL5 assembly assays, IL-6/STAT3 reporter assays, HIV infectivity assays The EMBO journal High 30166453
2021 AMBRA1 promotes TGFβ signaling as the substrate receptor of the CRL4 ubiquitin ligase complex, mediating nonproteolytic polyubiquitylation of Smad4 to enhance its transcriptional activity, thereby promoting TGFβ-induced EMT, migration, and invasion of breast cancer cells and metastasis in mouse models. Co-immunoprecipitation, in vitro ubiquitination assay, reporter gene assays, AMBRA1 knockdown/overexpression, mouse metastasis models Cancer research Medium 34362797
2021 AMBRA1 negatively regulates ALDH1B1 (a cancer stem cell marker) by mediating its K27- and K33-linked non-canonical ubiquitination in cooperation with TRAF6. Ubiquitination sites K506, K511, and K515 are important; ubiquitination-defective ALDH1B1 shows increased self-association, suggesting ubiquitination suppresses ALDH1B1 oligomerization. Co-immunoprecipitation, in vitro ubiquitination assay with ubiquitin linkage mapping (K27, K33), site-directed mutagenesis, self-association assays International journal of molecular sciences Medium 34769507
2022 Ambra1 deficiency in skeletal muscle (muscle-specific knockout) impairs mitophagic flux without affecting bulk autophagy, causing accumulation of TOMM20, swollen mitochondria, reduced mitochondrial membrane potential, decreased complex I activity, reduced recruitment of DRP1 and Parkin to mitochondria, and lysosomal accumulation. Overexpression of mitochondria-targeted Ambra1 in wild-type muscle is sufficient to enhance mitochondria clearance. Muscle-specific conditional Ambra1 knockout mice (Ambra1fl/fl:Mlc1f-Cre), in vivo Ambra1 overexpression, mitochondrial fractionation, electron microscopy, respiratory complex activity assay, mitophagy flux assays Journal of cachexia, sarcopenia and muscle High 35593053
2023 AMBRA1 is phosphorylated during mitosis by CDK1 and PLK1 on multiple sites. This phosphorylation is required for proper mitotic spindle orientation, mediated through NUMA1. AMBRA1 localization and/or dynamics of NUMA1 are strictly dependent on AMBRA1 presence, phosphorylation, and binding ability. Phosphorylation mapping during mitotic arrest, CDK1/PLK1 kinase assays, AMBRA1 phospho-mutant analysis, NUMA1 localization by imaging, spindle orientation assays Cellular and molecular life sciences Medium 37584777
2023 Cryo-EM structure of AMBRA1 in complex with DDB1 resolved at 3.08 Å. The N-terminal helix-loop-helix motif and WD40 domain of AMBRA1 associate with the double-propeller fold of DDB1, creating a scaffold for substrate recruitment. DDB1-binding-defective AMBRA1 mutants prevent Cyclin D1 ubiquitination in vitro and increase cell cycle progression. Cryo-EM structure determination, HDX-MS, in vitro ubiquitination assay, DDB1-binding mutagenesis, cell cycle assays Nature communications High 37993427
2022 AMBRA1 interacts with MAVS (mitochondrial antiviral signaling protein) at mitochondria and stabilizes MAVS by preventing its dsRNA-induced proteasomal degradation, thereby promoting dsRNA- and virus-induced apoptosis through a caspase-8-dependent pathway. Co-immunoprecipitation (AMBRA1–MAVS), AMBRA1 gene editing (knockout), proteasome inhibitor assays, apoptosis assays, Semliki Forest virus infection model Journal of cell science Medium 34859815
2024 BAG2, an effector of the ULK1 complex, regulates AMBRA1 subcellular localization. In nutrient-replete conditions, unphosphorylated BAG2 sequesters AMBRA1, attenuating autophagy. Upon starvation, ULK1 phosphorylates BAG2 at Ser31, which promotes AMBRA1 recruitment to the ER membrane and autophagy induction. Affinity purification-MS and proximity labeling-MS interactome of ULK1 complex subunits, Co-immunoprecipitation, BAG2 phospho-mutant (S31A), AMBRA1 localization imaging Cell reports Medium 39207901
2024 AMBRA1 promotes intestinal NF-κB-driven inflammation in an autophagy-independent manner by antagonizing the PP4R1/PP4c phosphatase complex: the N-terminal F1 domain of AMBRA1 competitively binds PP4R1, disrupting PP4R1/PP4c interaction with IKK and preventing IKK dephosphorylation. Upon TNF-α stimulation, IKKα phosphorylates AMBRA1 at S1043, impairing its CUL4A-mediated K48-linked ubiquitination and stabilizing AMBRA1. Co-immunoprecipitation (AMBRA1–PP4R1, AMBRA1–PP4c, AMBRA1–IKK), AMBRA1 domain deletion/mutagenesis (F1 domain, S1043), IKKα kinase assay, CUL4A ubiquitination assay, AMBRA1 conditional knockout mice Cell death and differentiation High 38424148
2025 In intestinal epithelial cells, AMBRA1 acts as a pro-oxidative factor by competitively binding NRF2 through its N-terminal F1 domain, antagonizing DUB3-mediated NRF2 deubiquitination and promoting NRF2 degradation. Under oxidative stress (H2O2), USP7 interaction with AMBRA1 is enhanced, leading to USP7-mediated deubiquitination of AMBRA1 at K83 and K86, stabilizing AMBRA1. Co-immunoprecipitation (AMBRA1–NRF2, AMBRA1–DUB3, AMBRA1–USP7), domain mutagenesis (F1 domain, K83/K86 sites), in vitro deubiquitination assay, AMBRA1 conditional knockout mice, IBD patient tissue analysis Advanced science Medium 39887666
2017 AMBRA1 binds α-synuclein phosphorylated at serine 129 with ~9-fold higher affinity than non-phosphorylated α-synuclein (in vitro and in vivo analyses). Silencing AMBRA1 function causes α-synuclein aggregates in the cytoplasm of mouse primary neurons, similar to the effect of the autophagy inhibitor Bafilomycin. Binding affinity assays (in vitro and in vivo), AMBRA1 knockdown in primary neurons, immunohistochemistry of human MSA brain samples Brain pathology Medium 27875637
2021 AMBRA1 suppresses SOCS3 in medulloblastoma Group 3 stem cells, enabling STAT3 activation. AMBRA1 expression depends on c-MYC levels, and AMBRA1 knockdown reduces stem potential, growth, and migration of MBGroup3 cells. Combined anti-autophagy and anti-STAT3 treatment impacts MBGroup3 outcome. AMBRA1 knockdown/overexpression, SOCS3 expression assays, STAT3 activation assays, tumor sphere formation, migration assays Acta neuropathologica Medium 34302498
2021 Loss of Ambra1 in melanoma promotes aggressiveness and metastasis by increasing cell motility/invasion, activating an EMT-like process, remodeling the extracellular matrix, and inducing hyperactivation of FAK1 signaling. FAK1 inhibition reduces cell invasion and melanoma growth in Ambra1-deficient cells. Ambra1-depleted Braf/Pten mouse melanoma model, invasion and migration assays, EMT marker analysis, FAK1 phosphorylation assays, FAK1 pharmacological inhibition Nature communications Medium 33953176

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Ambra1 regulates autophagy and development of the nervous system. Nature 837 17589504
2013 mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nature cell biology 650 23524951
2010 The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy. The Journal of cell biology 396 20921139
2018 HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα. Nature communications 232 30217973
2011 Parkin interacts with Ambra1 to induce mitophagy. The Journal of neuroscience : the official journal of the Society for Neuroscience 230 21753002
2011 Mitochondrial BCL-2 inhibits AMBRA1-induced autophagy. The EMBO journal 205 21358617
2014 AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nature cell biology 193 25438055
2012 Atg5 and Ambra1 differentially modulate neurogenesis in neural stem cells. Autophagy 144 22240590
2021 CRL4AMBRA1 is a master regulator of D-type cyclins. Nature 140 33854235
2021 The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. Nature 137 33854239
2014 AMBRA1 interplay with cullin E3 ubiquitin ligases regulates autophagy dynamics. Developmental cell 129 25499913
2021 AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity. Nature 126 33854232
2012 Proteolysis of Ambra1 during apoptosis has a role in the inhibition of the autophagic pro-survival response. Cell death and differentiation 116 22441670
2014 The autophagy regulators Ambra1 and Beclin 1 are required for adult neurogenesis in the brain subventricular zone. Cell death & disease 105 25188513
2015 Ambra1 at a glance. Journal of cell science 89 26034061
2012 Ambra1 at the crossroad between autophagy and cell death. Oncogene 86 23069654
2014 RNF2 is recruited by WASH to ubiquitinate AMBRA1 leading to downregulation of autophagy. Cell research 85 24980959
2014 Heterozygous ambra1 deficiency in mice: a genetic trait with autism-like behavior restricted to the female gender. Frontiers in behavioral neuroscience 81 24904333
2021 AMBRA1 regulates mitophagy by interacting with ATAD3A and promoting PINK1 stability. Autophagy 69 34798798
2020 Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs. Autophagy 69 33034545
2020 miR-103a-3p regulates mitophagy in Parkinson's disease through Parkin/Ambra1 signaling. Pharmacological research 68 32942015
2019 HUWE1 controls MCL1 stability to unleash AMBRA1-induced mitophagy. Cell death and differentiation 67 31434979
2018 AMBRA1-Mediated Mitophagy Counteracts Oxidative Stress and Apoptosis Induced by Neurotoxicity in Human Neuroblastoma SH-SY5Y Cells. Frontiers in cellular neuroscience 65 29755319
2021 Loss of Ambra1 promotes melanoma growth and invasion. Nature communications 58 33953176
2016 Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. Nature genetics 55 27723758
2011 Unleashing the Ambra1-Beclin 1 complex from dynein chains: Ulk1 sets Ambra1 free to induce autophagy. Autophagy 49 21079415
2018 AMBRA1 Controls Regulatory T-Cell Differentiation and Homeostasis Upstream of the FOXO3-FOXP3 Axis. Developmental cell 46 30513302
2013 Ambra1 knockdown in zebrafish leads to incomplete development due to severe defects in organogenesis. Autophagy 43 23348054
2017 MIR7-3HG, a MYC-dependent modulator of cell proliferation, inhibits autophagy by a regulatory loop involving AMBRA1. Autophagy 41 28059583
2017 Sexual dimorphism of AMBRA1-related autistic features in human and mouse. Translational psychiatry 41 28994820
2013 Expression of Ambra1 in mouse brain during physiological and Alzheimer type aging. Neurobiology of aging 41 23910655
2014 Ambra1 is an essential regulator of autophagy and apoptosis in SW620 cells: pro-survival role of Ambra1. PloS one 40 24587252
2020 HPV sensitizes OPSCC cells to cisplatin-induced apoptosis by inhibiting autophagy through E7-mediated degradation of AMBRA1. Autophagy 37 33172332
2017 Ambra1 spatially regulates Src activity and Src/FAK-mediated cancer cell invasion via trafficking networks. eLife 37 28362576
2015 Connecting autophagy: AMBRA1 and its network of regulation. Molecular & cellular oncology 36 27308402
2024 Role of AMBRA1 in mitophagy regulation: emerging evidence in aging-related diseases. Autophagy 35 39113560
2021 Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling. Acta neuropathologica 35 34302498
2018 Effects of caloric restriction on neuropathic pain, peripheral nerve degeneration and inflammation in normometabolic and autophagy defective prediabetic Ambra1 mice. PloS one 35 30532260
2017 AMBRA1, a novel α-synuclein-binding protein, is implicated in the pathogenesis of multiple system atrophy. Brain pathology (Zurich, Switzerland) 34 27875637
2016 Ambra1 in autophagy and apoptosis: Implications for cell survival and chemotherapy resistance. Oncology letters 34 27347152
2011 Ambra1: a Parkin-binding protein involved in mitophagy. Autophagy 34 21921694
2019 Ambra1 induces autophagy and desensitizes human prostate cancer cells to cisplatin. Bioscience reports 33 29101240
2018 Ambra1 modulates the sensitivity of breast cancer cells to epirubicin by regulating autophagy via ATG12. Cancer science 32 30027574
2015 AMBRA1 and BECLIN 1 interplay in the crosstalk between autophagy and cell proliferation. Cell cycle (Georgetown, Tex.) 31 25803737
2022 Ambra1 deficiency impairs mitophagy in skeletal muscle. Journal of cachexia, sarcopenia and muscle 30 35593053
2016 Prosurvival AMBRA1 turns into a proapoptotic BH3-like protein during mitochondrial apoptosis. Autophagy 30 27123694
2021 Nuclear factor I-C disrupts cellular homeostasis between autophagy and apoptosis via miR-200b-Ambra1 in neural tube defects. Cell death & disease 27 34930914
2019 A TRIM32-AMBRA1-ULK1 complex initiates the autophagy response in atrophic muscle cells. Autophagy 27 31234693
2018 Ambra1 Shapes Hippocampal Inhibition/Excitation Balance: Role in Neurodevelopmental Disorders. Molecular neurobiology 27 29488136
2022 Ambra1 regulates apoptosis and chemosensitivity in breast cancer cells through the Akt-FoxO1-Bim pathway. Apoptosis : an international journal on programmed cell death 25 35257265
2020 Rare mutations in the autophagy-regulating gene AMBRA1 contribute to human neural tube defects. Human mutation 24 32333458
2015 AMBRA1 and SQSTM1 expression pattern in prostate cancer. Apoptosis : an international journal on programmed cell death 24 26423274
2021 Deletion of the E3 ubiquitin ligase, Parkin, exacerbates chronic alcohol intake-induced cardiomyopathy through an Ambra1-dependent mechanism. British journal of pharmacology 23 33300167
2022 AMBRA1 and its role as a target for anticancer therapy. Frontiers in oncology 21 36237336
2021 AMBRA1 Promotes TGFβ Signaling via Nonproteolytic Polyubiquitylation of Smad4. Cancer research 21 34362797
2019 Neurodevelopmental Disorders: Functional Role of Ambra1 in Autism and Schizophrenia. Molecular neurobiology 20 30915711
2018 CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling. The EMBO journal 20 30166453
2023 Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation. Nature communications 19 37993427
2019 Autophagy and apoptosis are regulated by stress on Bcl2 by AMBRA1 in the endoplasmic reticulum and mitochondria. Theoretical biology & medical modelling 19 31665034
2016 shRNA-mediated AMBRA1 knockdown reduces the cisplatin-induced autophagy and sensitizes ovarian cancer cells to cisplatin. The Journal of toxicological sciences 19 26763392
2013 From gene to brain to behavior: schizophrenia-associated variation in AMBRA1 alters impulsivity-related traits. The European journal of neuroscience 19 23551272
2022 High-dose-androgen-induced autophagic cell death to suppress the Enzalutamide-resistant prostate cancer growth via altering the circRNA-BCL2/miRNA-198/AMBRA1 signaling. Cell death discovery 18 35318303
2022 Ambra1 haploinsufficiency in CD1 mice results in metabolic alterations and exacerbates age-associated retinal degeneration. Autophagy 18 35875981
2016 AMBRA1, a Novel BH3-Like Protein: New Insights Into the AMBRA1-BCL2-Family Proteins Relationship. International review of cell and molecular biology 18 28215535
2023 Ambra1 in exosomes secreted by HK-2 cells damaged by supersaturated oxalate induce mitophagy and autophagy-ferroptosis in normal HK-2 cells to participate in the occurrence of kidney stones. Biochimica et biophysica acta. Molecular cell research 16 37806389
2015 AMBRA1: When autophagy meets cell proliferation. Autophagy 16 26101901
2025 Redox-Induced Stabilization of AMBRA1 by USP7 Promotes Intestinal Oxidative Stress and Colitis Through Antagonizing DUB3-Mediated NRF2 Deubiquitination. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 15 39887666
2021 Melanoma secretion of transforming growth factor-β2 leads to loss of epidermal AMBRA1 threatening epidermal integrity and facilitating tumour ulceration. The British journal of dermatology 15 34773645
2015 AMBRA1-induced mitophagy: A new mechanism to cope with cancer? Molecular & cellular oncology 15 27308437
2024 The ULK1 effector BAG2 regulates autophagy initiation by modulating AMBRA1 localization. Cell reports 14 39207901
2023 Ambra1 modulates the tumor immune microenvironment and response to PD-1 blockade in melanoma. Journal for immunotherapy of cancer 13 36868570
2019 AMBRA1-mediated autophagy and apoptosis associated with an epithelial-mesenchymal transition in the development of cleft palate induced by all-trans retinoic acid. Annals of translational medicine 13 31157249
2012 Dismantling the autophagic arsenal when it is time to die: concerted AMBRA1 degradation by caspases and calpains. Autophagy 13 22575990
2024 Urolithin A attenuates Doxorubicin-induced cardiotoxicity by enhancing PINK1-regulated mitophagy via Ambra1. Chemico-biological interactions 12 39725191
2022 Ambra1 in cancer: implications for clinical oncology. Apoptosis : an international journal on programmed cell death 12 35994214
2021 AMBRA1 Negatively Regulates the Function of ALDH1B1, a Cancer Stem Cell Marker, by Controlling Its Ubiquitination. International journal of molecular sciences 12 34769507
2019 Ambra1 inhibits paclitaxel-induced apoptosis in breast cancer cells by modulating the Bim/mitochondrial pathway. Neoplasma 12 30784282
2015 AMBRA1-regulated autophagy in vertebrate development. The International journal of developmental biology 12 26374532
2024 AMBRA1 promotes intestinal inflammation by antagonizing PP4R1/PP4c mediated IKK dephosphorylation in an autophagy-independent manner. Cell death and differentiation 11 38424148
2022 The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma. Cell death & disease 11 36243772
2021 The Long-Lost Ligase: CRL4AMBRA1 Regulates the Stability of D-Type Cyclins. DNA and cell biology 11 34495753
2021 Aloe-emodin derivative produces anti-atherosclerosis effect by reinforcing AMBRA1-mediated endothelial autophagy. European journal of pharmacology 11 34800465
2021 The role of ambra1 in Pb-induced developmental neurotoxicity in zebrafish. Biochemical and biophysical research communications 11 35085890
2016 Nerve growth factor and autophagy: effect of nasal anti-NGF-antibodies administration on Ambra1 and Beclin-1 expression in rat brain. Growth factors (Chur, Switzerland) 11 26728403
2024 Src inhibition modulates AMBRA1-mediated mitophagy to counteract endothelial-to-mesenchymal transition in renal allograft fibrosis. Cell proliferation 9 38943534
2021 The pro-autophagic protein AMBRA1 coordinates cell cycle progression by regulating CCND (cyclin D) stability. Autophagy 9 34657573
2017 AMBRA1 is involved in T cell receptor-mediated metabolic reprogramming through an ATG7-independent pathway. Biochemical and biophysical research communications 9 28789945
2014 Ambra1 modulates starvation-induced autophagy through AMPK signaling pathway in cardiomyocytes. Biochemical and biophysical research communications 9 25117440
2024 Downregulation of Ambra1 by altered DNA methylation exacerbates dopaminergic neuron damage in a fenpropathrin-induced Parkinson-like mouse model. Ecotoxicology and environmental safety 8 38245935
2023 MiR-3653 blocks autophagy to inhibit epithelial-mesenchymal transition in breast cancer cells by targeting the autophagy-regulatory genes ATG12 and AMBRA1. Chinese medical journal 8 37464439
2023 AMBRA1 phosphorylation by CDK1 and PLK1 regulates mitotic spindle orientation. Cellular and molecular life sciences : CMLS 8 37584777
2022 AMBRA1 promotes dsRNA- and virus-induced apoptosis through interacting with and stabilizing MAVS. Journal of cell science 8 34859815
2019 Mitsugumin 53 promotes mitochondrial autophagy through regulating Ambra1 expression in C2C12 myoblast cells. Cell biology international 8 30614598
2019 AMBRA1, Autophagy, and the Extreme Male Brain Theory of Autism. Autism research and treatment 8 31687209
2025 Vitamin D sensitizes cervical cancer to radiation-induced apoptosis by inhibiting autophagy through degradation of Ambra1. Cell death discovery 7 39753527
2021 AMBRA1 has an impact on melanoma development beyond autophagy. Autophagy 7 34156327
2014 Autophagy regulation: RNF2 targets AMBRA1. Cell research 7 25104734
2023 Chemogenetic rectification of the inhibitory tone onto hippocampal neurons reverts autistic-like traits and normalizes local expression of estrogen receptors in the Ambra1+/- mouse model of female autism. Translational psychiatry 6 36804922
2023 Regulation of epidermal growth factor receptor tyrosine kinase inhibitor resistance via Ambra1-mediated autophagy in non-small cell lung cancer. Journal of physiology and pharmacology : an official journal of the Polish Physiological Society 6 37661184
2023 Autophagy genes AMBRA1 and ATG8 play key roles in midgut remodeling of the yellow fever mosquito, Aedes aegypti. Frontiers in insect science 6 38469502

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