Affinage

USP49

Ubiquitin carboxyl-terminal hydrolase 49 · UniProt Q70CQ1

Length
688 aa
Mass
79.2 kDa
Annotated
2026-06-11
20 papers in source corpus 19 papers cited in narrative 19 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

USP49 is a deubiquitinating enzyme that acts both at chromatin and on individual protein substrates to control gene expression, genome integrity, and signaling (PMID:23824326, PMID:28363942). Its founding activity is the specific removal of monoubiquitin from histone H2B as part of a complex with RVB1 and SUG1, which controls cotranscriptional splicing of a large set of exons and modulates nucleosome stability (PMID:23824326). This chromatin-directed H2B deubiquitination extends to gene-specific regulation: USP49 binds the MDM2 promoter and removes H2Bub there, restraining MDM2 transcription and thereby de-repressing p53 target genes (PMID:35072515). Beyond chromatin, USP49 stabilizes diverse substrates by reversing their ubiquitination — it deubiquitinates and stabilizes FKBP51 to promote PHLPP-mediated dephosphorylation of AKT-Ser473 (PMID:28363942), removes K63-linked ubiquitin from MITA/STING to block TBK1 recruitment and dampen type I interferon responses (PMID:30943264), and stabilizes APOBEC3G to enhance its anti-HIV-1 activity (PMID:31397674). USP49 also engages the DNA damage response, interacting with and deubiquitinating p53 in a p53-induced positive feedback loop, with Usp49-knockout mice showing increased susceptibility to colon tumors (PMID:29748582). Functionally, loss of USP49 impairs proliferation, increases aneuploidy, and permits override of the nocodazole-induced spindle assembly checkpoint (PMID:36702832). USP49 protein level is itself controlled by ubiquitin-proteasome turnover through the Fbxo45/NEK6 axis (PMID:35279684).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2013 High

    Established USP49 as a histone H2B-specific deubiquitinase and linked this chromatin activity to a cellular process — cotranscriptional pre-mRNA splicing.

    Evidence Biochemical purification, in vitro DUB assay, Co-IP defining an RVB1/SUG1 complex, and ChIP/RNA-seq after knockdown

    PMID:23824326

    Open questions at the time
    • Structural basis of H2B recognition not resolved
    • How splicing factor association is mechanistically coupled to uH2B removal not fully defined
  2. 2017 High

    Extended USP49 activity beyond chromatin to a signaling substrate, showing it stabilizes FKBP51 to suppress AKT activation.

    Evidence Reciprocal Co-IP, in vivo ubiquitination assay, and pathway epistasis with AKT-Ser473 readout in pancreatic cancer cells

    PMID:28363942

    Open questions at the time
    • Whether USP49 directly deubiquitinates FKBP51 in vitro not shown
    • Ubiquitin linkage specificity on FKBP51 not defined
  3. 2018 Medium

    Placed USP49 in the DNA damage response as a p53 stabilizer within a feed-forward loop, with tumor-suppressive consequences in vivo.

    Evidence DUB library screen, Co-IP, in vivo ubiquitination assay, and AOM/DSS tumorigenesis in Usp49-knockout mice

    PMID:29748582

    Open questions at the time
    • Direct in vitro deubiquitination of p53 not reconstituted
    • Relationship to chromatin-based MDM2 regulation not integrated at this stage
  4. 2018 Medium

    Showed substrate stabilization as a recurring mode, with USP49 protecting DUSP1 to restrain JNK signaling and apoptosis in cardiomyocytes.

    Evidence Co-IP, ubiquitination analysis, and JNK/apoptosis readouts with an in vivo rat I/R model

    PMID:30246457

    Open questions at the time
    • No in vitro deubiquitination reconstitution
    • Tissue specificity of the DUSP1 interaction not established
  5. 2019 High

    Defined a linkage-specific role in innate immunity, with USP49 stripping K63 chains from MITA/STING to limit antiviral signaling.

    Evidence Reciprocal Co-IP, K63-linkage deubiquitination assay, MITA aggregation and TBK1 recruitment assays, and Usp49-/- mice resistant to HSV-1

    PMID:30943264

    Open questions at the time
    • Whether the same complex partners (RVB1/SUG1) participate not addressed
    • Structural mechanism of MITA aggregation control unknown
  6. 2019 Medium

    Showed USP49 can promote antiviral restriction by stabilizing APOBEC3G against a Vif/cullin-independent degradation route.

    Evidence Co-IP, in vitro deubiquitination assay, and A3G stability/HIV replication readouts

    PMID:31397674

    Open questions at the time
    • Identity of the Vif-independent degradation pathway not defined
    • Physiological context in primary cells not tested
  7. 2022 Medium

    Connected USP49 chromatin H2B-DUB activity to gene-specific transcriptional control of the p53 axis via the MDM2 promoter.

    Evidence ChIP and H2Bub ChIP at MDM2, RT-PCR of p53 targets, and KO/overexpression in HCT116

    PMID:35072515

    Open questions at the time
    • How USP49 is recruited to specific promoters unknown
    • Generality across other promoters not mapped
  8. 2022 Medium

    Identified the mechanism controlling USP49 abundance, showing an Fbxo45 SCF complex enhanced by NEK6 drives its K48-linked proteasomal degradation.

    Evidence Co-IP with SPRY-domain mapping, ubiquitination assay, cycloheximide chase, NEK6 kinase assay, and xenograft

    PMID:35279684

    Open questions at the time
    • Signals controlling Fbxo45 engagement of USP49 unknown
    • Whether degradation is context- or substrate-dependent unresolved
  9. 2022 Medium

    Linked USP49 to DSB repair pathway choice by showing it deubiquitinates K15-ubiquitylated gamma-H2AX and limits 53BP1 recruitment.

    Evidence Catalytic-dead mutant interaction/colocalization, ubiquitination assay, 53BP1 foci assay, and proteasome inhibitor analysis

    PMID:35598681

    Open questions at the time
    • Endogenous timing of gamma-H2AX deubiquitination during repair not resolved
    • Balance with the p53-stabilizing role not reconciled
  10. 2022 Medium

    Showed USP49 stabilizes BAG2 downstream of c-MYC transcriptional activation to promote colorectal cancer survival and chemoresistance.

    Evidence Promoter analysis of c-MYC binding, Co-IP, ubiquitination assay, and proliferation/chemoresistance readouts

    PMID:35367823

    Open questions at the time
    • No in vitro deubiquitination reconstitution
    • Direct versus indirect stabilization of BAG2 not separated
  11. 2023 Medium

    Defined a cell-division phenotype for USP49 loss — proliferation defects, aneuploidy, and SAC override — and expanded its interactome.

    Evidence siRNA/shRNA knockdown, nocodazole SAC and aneuploidy assays, and MS-based interactome (ribophorin 1, USP44, centrins)

    PMID:36702832

    Open questions at the time
    • Substrate mediating the SAC phenotype not identified
    • Functional significance of new interactors not validated
  12. 2025 Low

    Proposed a DSB-localized condensate model in which ATM-driven LLPS recruits USP49 to deubiquitinate RPA70 and promote homologous recombination.

    Evidence LLPS assay, IR-induced foci, Co-IP, ubiquitination assay, and HR repair readouts in ESCC with xenograft

    PMID:40460957

    Open questions at the time
    • LLPS and HR claims await independent validation
    • Reconciliation with the earlier 53BP1-restraining DSB role unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How USP49 selects among its many candidate substrates across chromatin, signaling, immunity, and DNA repair contexts — and which interactions are direct, in vitro-reconstituted deubiquitination events versus inferred stabilizations — remains unresolved.
  • Substrate-targeting determinants and recruitment mechanisms undefined
  • Many proposed substrates rest on Co-IP plus cellular ubiquitination assays without enzymatic reconstitution
  • No structural model of USP49 with any substrate

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016787 hydrolase activity 2 GO:0042393 histone binding 2
Localization
GO:0005634 nucleus 2 GO:0000228 nuclear chromosome 1
Pathway
R-HSA-392499 Metabolism of proteins 2 R-HSA-168256 Immune System 1 R-HSA-73894 DNA Repair 1 R-HSA-8953854 Metabolism of RNA 1
Partners
APOBEC3GFBXO45FKBP51MDM2RVB1STING1SUG1TP53
Complex memberships
USP49-RVB1-SUG1 H2B-deubiquitinase complex

Evidence

Reading pass · 19 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 USP49 is a histone H2B-specific deubiquitinase that forms a complex with RuvB-like1 (RVB1) and SUG1, deubiquitinates histone H2B in vitro and in vivo, and is required for efficient cotranscriptional splicing of a large set of exons. USP49 knockdown increased H2B ubiquitination (uH2B) at affected exons and upstream/downstream intronic splicing elements, and altered U1A and U2B association with chromatin and nascent pre-mRNA. Elevated uH2B also increased nucleosome stability at these exons. Biochemical purification, in vitro deubiquitinase assay, Co-IP (complex with RVB1/SUG1), RNA-seq (>9000 isoform changes), ChIP, siRNA knockdown Genes & development High 23824326
2017 USP49 deubiquitinates and stabilizes FKBP51, which in turn enhances PHLPP-mediated dephosphorylation of AKT at Ser473, thereby negatively regulating AKT activation. USP49 inhibited pancreatic cancer cell proliferation and enhanced gemcitabine sensitivity in a FKBP51-AKT-dependent manner. Co-IP, in vivo ubiquitination assay, knockdown/overexpression with AKT phosphorylation readout, epistasis rescue experiments The EMBO journal High 28363942
2018 USP49 interacts with the N-terminus of p53, deubiquitinates p53 (suppressing multiple forms of its ubiquitination), and stabilizes p53 protein. USP49 expression is transcriptionally upregulated by p53 in response to DNA damage, forming a positive feedback loop. USP49 knockout mice are more susceptible to AOM/DSS-induced colon tumors. DUB library screen, Co-IP, in vivo ubiquitination assay, KO mouse model, etoposide sensitivity assay Cell death & disease Medium 29748582
2018 USP49 directly interacts with DUSP1 and deubiquitinates it, thereby stabilizing DUSP1 protein. Stabilized DUSP1 dephosphorylates JNK1/2, and this USP49-DUSP1-JNK1/2 axis protects cardiomyocytes from ischemia-reperfusion-induced apoptosis. Co-immunoprecipitation, ubiquitination analysis, overexpression/knockdown with JNK phosphorylation and apoptosis readouts, in vivo rat I/R model (TUNEL) Journal of cellular physiology Medium 30246457
2019 USP49 interacts with MITA/STING and removes K63-linked ubiquitin chains from MITA after HSV-1 infection, inhibiting MITA aggregation and subsequent recruitment of TBK1 to the signaling complex, thereby attenuating type I interferon and proinflammatory cytokine production. Usp49-/- mice exhibit resistance to lethal HSV-1 infection. Co-IP, in vivo K63-linked deubiquitination assay, MITA aggregation assay, TBK1 recruitment assay, siRNA/CRISPR KO, Usp49-/- mouse model PLoS pathogens High 30943264
2019 USP49 directly interacts with APOBEC3G (A3G) and removes ubiquitin from it, stabilizing A3G protein and enhancing its anti-HIV-1 activity. USP49 also counteracts a Vif- and cullin-ring-independent pathway of A3G degradation. Co-IP, in vitro deubiquitination assay, overexpression/knockdown with A3G stability and HIV replication readouts eLife Medium 31397674
2022 Fbxo45, an F-box protein forming an atypical SCF E3 ligase complex, directly binds USP49 through its SPRY domain and mediates K48-linked ubiquitination and proteasomal degradation of USP49. This Fbxo45-mediated USP49 degradation is enhanced by NEK6 kinase. Loss of Fbxo45 stabilizes USP49, inhibiting pancreatic cancer cell viability and motility. Co-IP, ubiquitination assay, cycloheximide chase, NEK6 kinase assay, xenograft mouse model Cell death & disease Medium 35279684
2022 USP49 is transcriptionally activated by c-MYC and deubiquitinates BAG2, stabilizing it to promote CRC cell survival and chemoresistance. Promoter analysis (c-MYC binding), Co-IP, ubiquitination assay, knockdown/overexpression with proliferation and chemoresistance readouts Biochemical and biophysical research communications Medium 35367823
2022 USP49 deubiquitinates γH2AX (ubiquitylated at K15); a catalytic-dead USP49 mutant interacts with and colocalizes with γH2AX. Overexpressed USP49 suppressed γH2AX ubiquitylation, inhibited 53BP1 foci formation at DSBs, and increased cell sensitivity to DSB-inducing drugs. Endogenous USP49 is degraded via the proteasome upon DSB induction. Overexpression and catalytic mutant analysis, Co-IP, immunofluorescence colocalization, ubiquitination assay, 53BP1 foci formation assay, proteasome inhibitor treatment Gene Medium 35598681
2022 USP49 directly binds the MDM2 gene promoter (by ChIP) and deubiquitinates H2B at this locus; USP49 knockout increases H2Bub enrichment at the MDM2 gene, elevating MDM2 transcription and suppressing p53 target gene expression, thereby promoting HCT116 cell proliferation. ChIP, H2Bub ChIP, RT-PCR for p53 target genes, KO and overexpression Molecular and cellular biology Medium 35072515
2021 USP49 is a GRβ-binding protein and the interaction depends on GRβ ubiquitination status. USP49 knockdown in glioblastoma cells increased GRβ ubiquitination and amplified GRβ oncogenic effects, indicating USP49 modulates GRβ stability through deubiquitination. Co-IP, ubiquitination assay, K733R GRβ mutant, siRNA knockdown with proliferation/invasion/apoptosis readouts Molecular cancer research : MCR Low 34610959
2023 USP49 loss impairs cancer cell proliferation, increases aneuploidy, and allows cells to override the spindle assembly checkpoint (SAC) arrest induced by nocodazole. New binding partners of USP49 identified include ribophorin 1, USP44, and different centrins. siRNA/shRNA knockdown, nocodazole SAC assay, aneuploidy measurement, MS-based interactome (binding partners) Cell death & disease Medium 36702832
2024 USP49 stabilizes SIRT1 by inhibiting its ubiquitination and degradation, thereby promoting autophagy and carboplatin resistance in retinoblastoma cells. IGF2BP3-mediated m6A modification upregulates USP49 expression in an m6A-dependent manner. Co-IP, ubiquitination assay, autophagy flux assay, IGF2BP3 m6A-dependent regulation assay, rescue experiments, xenograft model The Kaohsiung journal of medical sciences Low 39497328
2024 USP49 binds IκBα and mediates its deubiquitination, leading to IκBα stabilization, cytoplasmic retention of NF-κB, and suppression of NF-κB activity. miR-361-3p inhibits USP49 expression by binding its 3' UTR, relieving IκBα deubiquitination and thus activating NF-κB to promote inflammation and apoptosis in sepsis-induced myocardial injury. Co-immunoprecipitation, western blot, dual-luciferase reporter (miR-361-3p/Usp49 3'UTR), CLP rat model, LPS cell model Toxicology research Low 39568464
2025 USP49 interacts with HDAC3 (validated by IP-mass spectrometry and Co-IP); USP49 downregulation augments HDAC3 ubiquitination, reducing HDAC3 protein stability. In the context of cold atmospheric plasma treatment, reduced USP49 destabilizes HDAC3, altering H3K18 lactylation and p53-driven ferroptosis in endometrial cancer. Immunoprecipitation-mass spectrometry, Co-IP, immunofluorescence co-localization, molecular docking, ubiquitination assay, xenograft model Journal of translational medicine Low 40234906
2025 ATM promotes liquid-liquid phase separation (LLPS) of USP49 and its recruitment to DNA double-strand breaks upon ionizing radiation. USP49 deubiquitinates RPA70 and recruits it along with Rad51 to DSBs, promoting homologous recombination repair and radioresistance in ESCC. p53 further augments USP49 transcription upon IR. LLPS assay, IR-induced DSB foci (immunofluorescence), Co-IP, ubiquitination assay, HR repair assay, knockdown/overexpression in vivo xenograft International journal of biological macromolecules Low 40460957
2025 USP49 interacts with PKMYT1 and limits its ubiquitination and proteasomal degradation, thereby stabilizing PKMYT1 and promoting G2/M cell cycle progression and malignant phenotypes in triple-negative breast cancer cells. Co-IP, ubiquitination assay, knockdown/overexpression with cell cycle and viability readouts, PKMYT1 rescue experiments Biochemical and biophysical research communications Low 41443044
2025 USP49 interacts with and deubiquitinates GRPR (gastrin-releasing peptide receptor), stabilizing it and promoting PI3K/AKT-driven tumor survival in medullary thyroid carcinoma. The natural flavonoid vitexin inhibits USP49, thereby destabilizing GRPR. Co-IP, ubiquitination assay, vitexin treatment with GRPR stability and AKT signaling readouts, xenograft mouse model Biochimica et biophysica acta. Molecular basis of disease Low 41349242
2025 FBXO2 E3 ubiquitin ligase directly binds USP49 and targets it for ubiquitin-mediated proteasomal degradation, reducing USP49 stability and function in hepatocellular carcinoma cells. Co-IP, in vivo ubiquitination assay, cycloheximide chase, siRNA knockdown rescue experiments, xenograft model Frontiers in immunology Low 41035649

Source papers

Stage 0 corpus · 20 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 USP49 negatively regulates tumorigenesis and chemoresistance through FKBP51-AKT signaling. The EMBO journal 91 28363942
2013 USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. Genes & development 85 23824326
2022 Fbxo45 facilitates pancreatic carcinoma progression by targeting USP49 for ubiquitination and degradation. Cell death & disease 57 35279684
2019 USP49 negatively regulates cellular antiviral responses via deconjugating K63-linked ubiquitination of MITA. PLoS pathogens 46 30943264
2018 USP49 participates in the DNA damage response by forming a positive feedback loop with p53. Cell death & disease 40 29748582
2019 USP49 potently stabilizes APOBEC3G protein by removing ubiquitin and inhibits HIV-1 replication. eLife 27 31397674
2022 c-MYC-USP49-BAG2 axis promotes proliferation and chemoresistance of colorectal cancer cells in vitro. Biochemical and biophysical research communications 25 35367823
2018 USP49 inhibits ischemia-reperfusion-induced cell viability suppression and apoptosis in human AC16 cardiomyocytes through DUSP1-JNK1/2 signaling. Journal of cellular physiology 25 30246457
2020 The long non-coding RNA HLNC1 potentiates hepatocellular carcinoma progression via interaction with USP49. Journal of clinical laboratory analysis 13 32691951
2025 Cold atmospheric plasma drives USP49/HDAC3 axis mediated ferroptosis as a novel therapeutic strategy in endometrial cancer via reinforcing lactylation dependent p53 expression. Journal of translational medicine 11 40234906
2021 Oncogenic Activity of Glucocorticoid Receptor β Is Controlled by Ubiquitination-Dependent Interaction with USP49 in Glioblastoma Cells. Molecular cancer research : MCR 11 34610959
2022 USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair. Gene 9 35598681
2022 USP49-Mediated Histone H2B Deubiquitination Regulates HCT116 Cell Proliferation through MDM2-p53 Axis. Molecular and cellular biology 6 35072515
2024 IGF2BP3-dependent N6-methyladenosine modification of USP49 promotes carboplatin resistance in retinoblastoma by enhancing autophagy via regulating the stabilization of SIRT1. The Kaohsiung journal of medical sciences 4 39497328
2025 USP49 undergoes liquid-liquid phase separation and stabilizes RPA70 to induce radioresistance through homologous recombination repair in esophageal squamous cell carcinoma. International journal of biological macromolecules 3 40460957
2024 miR-361-3p overexpression promotes apoptosis and inflammation by regulating the USP49/IκBα/NF-κB pathway to aggravate sepsis-induced myocardial injury. Toxicology research 3 39568464
2025 FBXO2 promotes hepatocellular carcinoma progression and sorafenib resistance by targeting USP49 for proteasomal degradation. Frontiers in immunology 2 41035649
2023 USP49 deubiquitinase regulates the mitotic spindle checkpoint and prevents aneuploidy. Cell death & disease 1 36702832
2025 Vitexin targets USP49-GRPR deubiquitination axis in medullary thyroid carcinoma therapy. Biochimica et biophysica acta. Molecular basis of disease 0 41349242
2025 USP49 promotes the malignancy of triple-negative breast cancer cells by regulating PKMYT1 ubiquitination and stability. Biochemical and biophysical research communications 0 41443044

Missed literature

Know a paper Affinage missed for USP49? Flag it for the maintainers and the community.

No submissions yet.