Affinage

GNL3

Guanine nucleotide-binding protein-like 3 · UniProt Q9BVP2

Length
549 aa
Mass
62.0 kDa
Annotated
2026-06-10
22 papers in source corpus 10 papers cited in narrative 10 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/5 claims corpus-supported (80%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

GNL3 (nucleostemin) is a nucleolar GTP-binding protein that operates across ribosome biogenesis, genome integrity, and cell-cycle/oncogenic signaling (PMID:16803892, PMID:37965896, PMID:41772945). In ribosome biogenesis, work on the yeast ortholog Nug1 established a modular architecture in which an N-terminal RNA-binding domain mediates nucleolar targeting and association with pre-60S particles, a circularly permuted GTPase domain hydrolyzes GTP, and the C-terminal domain is essential for biogenesis (PMID:16803892); this GTPase activity is stimulated by potassium, and Nug1 binds the RNA helicase Dbp10 at overlapping sites near helix H89 of the nascent peptidyl transferase center, with Nug1 depletion or nucleotide-binding mutation causing loss of Dbp10 from early pre-60S particles (PMID:26823502). In genome maintenance, GNL3 sequesters the replication initiation factor ORC2 in the nucleolus to limit origin firing and prevent RPA exhaustion and nuclease-dependent resection of stalled forks (PMID:37965896), whereas SUMOylation at K196 (written by USP36, erased by SENP3) licenses GNL3 to engage the BLM-DNA2 helicase-nuclease complex through SUMO-interacting motifs and promote end resection, RPA and RAD51 loading during homologous recombination (PMID:41279596). In cancer signaling, GNL3 promotes nucleolar polyubiquitylation and inactivation of the CDK inhibitor p27kip1, releasing CDK2-Cyclin E activity (PMID:27998760), and acts as a dual coregulator of the androgen receptor, coactivating proliferation genes NEK2 and CDC20 while corepressing immune genes CXCL10 and TAP1 via class I HDACs in castration-resistant prostate cancer (PMID:41772945). GNL3 is itself a node in a p53 axis: lactylation at Lys-5 promotes binding by nuclear ENO2, which displaces MDM2 from GNL3, stabilizing p53 and driving chondrocyte senescence (PMID:42192505), and its expression is transcriptionally activated by XBP1 (PMID:30936750).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2006 High

    Established the domain logic of the GNL3 ortholog, defining which regions confer nucleolar targeting, GTP hydrolysis, and essentiality in ribosome biogenesis.

    Evidence Domain deletion analysis, in vitro GTPase assay, and genetic epistasis with pre-60S factors in yeast Nug1

    PMID:16803892

    Open questions at the time
    • Did not identify the substrate/effector of the GTPase activity
    • Human GNL3 architecture inferred from yeast ortholog
  2. 2016 High

    Resolved how the GTPase couples to ribosome assembly, showing K⁺-stimulated GTPase activity and direct binding to the Dbp10 helicase at the peptidyl transferase center.

    Evidence In vitro reconstitution of Nug1-Dbp10 interaction, enzymatic GTPase assay, and in vivo rRNA-protein crosslinking with mutant validation

    PMID:26823502

    Open questions at the time
    • Mechanism by which GTP hydrolysis triggers Dbp10 release not defined
    • Conservation of the K⁺-stimulation in human GNL3 not tested here
  3. 2016 Medium

    Connected GNL3 to cell-cycle control by showing it drives nucleolar polyubiquitylation that inactivates the CDK inhibitor p27kip1.

    Evidence Subcellular fractionation, reciprocal co-IP of p27 with NS, ubiquitylation and CDK2 activity assays with siRNA knockdown in hepatocellular carcinoma cells

    PMID:27998760

    Open questions at the time
    • E3 ligase responsible for p27 ubiquitylation not identified
    • Whether GTPase activity is required for this function untested
  4. 2019 Medium

    Placed GNL3 downstream of a transcriptional regulator by showing XBP1 binds the GNL3 promoter and that GNL3 is required for XBP1-driven proliferation and invasion.

    Evidence Dual-luciferase reporter assay, siRNA knockdown, and overexpression rescue in osteosarcoma cells

    PMID:30936750

    Open questions at the time
    • Downstream effectors of GNL3 in the XBP1 axis not defined
    • Single cell-context
  5. 2022 Low

    Linked GNL3 to stem-like tumor properties through SIRT1, though without a direct regulatory mechanism.

    Evidence siRNA knockdown with SIRT1 Western blot, proliferation/invasion assays, and a subcutaneous xenograft model

    PMID:35432540

    Open questions at the time
    • No direct mechanistic link (ChIP/reporter) between GNL3 and SIRT1 transcription
    • Single lab, single readout
  6. 2023 High

    Defined a genome-protective role in which GNL3 sequesters ORC2 to restrain origin firing and prevent RPA exhaustion and fork resection.

    Evidence DNA fiber resection assay, reciprocal GNL3-ORC2 co-IP, nucleolar fractionation, and origin-firing inhibition rescue

    PMID:37965896

    Open questions at the time
    • How GNL3 nucleolar concentration is dynamically regulated during replication stress unclear
    • Structural basis of GNL3-ORC2 binding unknown
  7. 2025 Medium

    Showed that SUMOylation of GNL3 at K196 is the switch that recruits the BLM-DNA2 complex to drive homologous-recombination end resection.

    Evidence SUMOylation assays with K196R mutant, co-IP of GNL3 with BLM-DNA2, RPA/RAD51 loading assays, SENP3/USP36 manipulation, and breast cancer variant analysis (preprint)

    PMID:41279596

    Open questions at the time
    • Preprint, not yet peer reviewed
    • Apparent opposite effect on resection versus the ORC2 pathway not reconciled
    • Functional impact of breast cancer variants in vivo untested
  8. 2026 Medium

    Established GNL3 as a dual transcriptional coregulator of the androgen receptor, simultaneously activating proliferation genes and repressing immune genes in castration-resistant prostate cancer.

    Evidence Proteomic profiling, reciprocal GNL3-AR co-IP, chromatin occupancy and reporter assays, knockdown with proliferation/metastasis/CD8+ T cell readouts

    PMID:41772945

    Open questions at the time
    • Whether GTPase or nucleolar functions are required for AR coregulation unknown
    • Direct corepressor recruitment mechanism at immune gene loci not fully defined
  9. 2026 High

    Defined GNL3 as a p53-regulatory node in which Lys-5 lactylation recruits ENO2 to displace MDM2, stabilizing p53 and driving chondrocyte senescence.

    Evidence Co-IP, GST pull-down, site-directed mutagenesis (E4A-ENO2, K5R-GNL3), lactylomics, and an in vivo mouse osteoarthritis model with ENO2 inhibitor

    PMID:42192505

    Open questions at the time
    • How GNL3-MDM2 binding is coupled to MDM2 destabilization mechanistically unclear
    • Relevance of the lactylation axis outside chondrocytes untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how GNL3's conserved nucleolar GTPase/ribosome-biogenesis activity mechanistically connects to its diverse roles in DNA replication, HR repair, p27/p53 regulation, and AR transcription.
  • No structural model unifying the GTPase domain with the genome-integrity and transcriptional functions
  • Whether nucleotide binding is required for the non-ribosomal functions untested
  • Apparent opposing roles in limiting versus promoting resection unreconciled

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003924 GTPase activity 2 GO:0098772 molecular function regulator activity 2 GO:0003723 RNA binding 1 GO:0140110 transcription regulator activity 1
Localization
GO:0005730 nucleolus 3 GO:0005634 nucleus 1
Pathway
R-HSA-73894 DNA Repair 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-1640170 Cell Cycle 1 R-HSA-74160 Gene expression (Transcription) 1
Partners
ARBLMDBP10DNA2MDM2ORC2SENP3USP36

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 Yeast Nug1 (ortholog of GNL3) contains an N-terminal RNA-binding domain that is sufficient and necessary for nucleolar/nuclear targeting and association with pre-60S ribosomal particles; the middle circularly permuted GTPase domain has intrinsic GTP hydrolysis activity in vitro but is not essential for cell growth; the C-terminal domain is essential for ribosome biogenesis. Domain deletion analysis, in vitro GTPase assay, genetic epistasis with pre-60S factors Noc2, Noc3, and Dbp10 The Journal of biological chemistry High 16803892
2016 Yeast Nug1/GNL3 exhibits low intrinsic GTPase activity that is stimulated by potassium ions (K⁺-dependent GTPase). Nug1 physically interacts with the RNA helicase Dbp10, and this interaction was reconstituted in vitro using Chaetomium thermophilum orthologs. In vivo rRNA-protein crosslinking showed Nug1 and Dbp10 bind at proximal and partially overlapping sites on the pre-60S ribosome, prominently at helix H89 that forms part of the peptidyl transferase center (PTC). Depletion of Nug1 or expression of a nucleotide-binding mutant causes loss of Dbp10 from early pre-60S particles. In vitro enzymatic GTPase assay, in vitro reconstitution of Nug1-Dbp10 interaction, in vivo rRNA-protein crosslinking, depletion and nucleotide-binding mutant analysis Nucleic acids research High 26823502
2016 GNL3/nucleostemin (NS) promotes nucleolar polyubiquitylation of the CDK inhibitor p27kip1 in hepatocellular carcinoma cells; subcellular fractionation showed nucleolar p27 has significantly higher polyubiquitylation than nucleoplasmic p27; depletion of NS inhibited nucleolar polyubiquitylation of p27, leading to increased binding of p27 to CDK2-Cyclin E complex and CDK2 inhibition with consequent cell cycle arrest. Subcellular fractionation, co-immunoprecipitation of p27 with NS, ubiquitylation assay, CDK2 activity assay, siRNA knockdown Cancer letters Medium 27998760
2019 XBP1 transcription factor binds to the GNL3 promoter (demonstrated by dual-luciferase reporter assay) and activates GNL3 expression; XBP1 overexpression rescues the inhibitory effects on proliferation, invasion, and EMT caused by GNL3 knockdown in osteosarcoma cells, placing GNL3 downstream of XBP1. Dual-luciferase reporter assay, siRNA knockdown, overexpression rescue experiment Cancer management and research Medium 30936750
2023 Human GNL3/nucleostemin prevents nuclease-dependent resection of nascent DNA at stalled replication forks by limiting origin firing; GNL3 interacts with the DNA replication initiation factor ORC2 in the nucleolus, and GNL3 depletion causes excess origin firing and exhaustion of available RPA, driving DNA resection. GNL3 concentration in the nucleolus is required to sequester ORC2 and limit replication stress-induced DNA resection. DNA fiber assay (nascent DNA resection), co-immunoprecipitation of GNL3 and ORC2, live-cell imaging/fractionation showing nucleolar localization, inhibition of origin firing rescue experiment EMBO reports High 37965896
2021 GNL3 knockdown in HeLa cells down-regulates expression of IL24 and PTN as determined by RNA-seq; this was validated in the chondrosarcoma cell line SW1353, positioning GNL3 as an upstream regulator of IL24 and PTN transcription. RNA-seq after shRNA-mediated GNL3 knockdown, validated by qRT-PCR in SW1353 cells Life sciences Low 33358901
2025 GNL3 undergoes SUMOylation at K196, mediated by the nucleolar deubiquitinating enzyme USP36 acting as a SUMO ligase, and deSUMOylated by SENP3. SUMOylated GNL3 interacts with the BLM-DNA2 helicase-nuclease complex via SUMO-interacting motifs (SIMs) in both proteins, promoting DNA end resection, RPA loading, and RAD51 loading for homologous recombination (HR) repair. A SUMO-defective K196R mutant fails to rescue DNA damage response induced by endogenous GNL3 knockdown. Several breast cancer-derived GNL3 variants that disrupt SUMOylation or SIM fail to interact with BLM-DNA2. SUMOylation assay with wild-type and K196R mutant, co-immunoprecipitation of GNL3 with BLM-DNA2, DNA end resection assay, RPA/RAD51 loading assay, SENP3 and USP36 functional experiments, breast cancer variant analysis bioRxivpreprint Medium 41279596
2026 GNL3 physically interacts with the androgen receptor (AR), enhances AR chromatin occupancy, and coactivates transcription of proliferation genes NEK2 and CDC20 in castration-resistant prostate cancer (CRPC). Concurrently, GNL3 functions as a corepressor of immune-responsive genes (CXCL10, TAP1) via class I HDACs, enabling CD8+ T cell elimination and immunosuppressive tumor microenvironment. AR-GNL3 complex formation increases from primary PCa to CRPC. Proteomic profiling, co-immunoprecipitation of GNL3 with AR, chromatin occupancy assay, transcriptional reporter assays, GNL3 knockdown in CRPC cells with functional readouts (proliferation, metastasis, CD8+ T cell assay) Advanced science Medium 41772945
2026 Nuclear ENO2 binds GNL3 lactylated at Lys-5 (mediated by ENO2 Glu-4 residue), displacing MDM2 from GNL3. This results in MDM2 destabilization, impaired p53 ubiquitination, p53 accumulation, and chondrocyte senescence. p53 in turn transcriptionally activates ENO2, forming a positive feedback loop. Pharmacological inhibition of ENO2 restores p53 degradation and mitigates OA in aged mice. Co-immunoprecipitation, GST pull-down, site-directed mutagenesis (E4A-ENO2 and K5R-GNL3 mutants), lactylomics, in vivo mouse OA model with intra-articular ENO2 inhibitor injection Cellular & molecular biology letters High 42192505
2022 GNL3 regulates SIRT1 expression in hepatocellular carcinoma cells, and mediates stem cell-like properties of HCC cells through SIRT1; silencing GNL3 inhibits proliferation, migration, and invasion of HCC cells in vitro and reduces tumor growth in vivo. siRNA knockdown of GNL3, Western blot for SIRT1, CCK-8 and Transwell assays, subcutaneous tumor-bearing animal model Journal of oncology Low 35432540

Source papers

Stage 0 corpus · 22 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 The NUG1 GTPase reveals and N-terminal RNA-binding domain that is essential for association with 60 S pre-ribosomal particles. The Journal of biological chemistry 51 16803892
2002 Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein science : a publication of the Protein Society 49 12441390
2015 GNL3 and SKA3 are novel prostate cancer metastasis susceptibility genes. Clinical & experimental metastasis 44 26429724
2017 Upregulation of GNL3 expression promotes colon cancer cell proliferation, migration, invasion and epithelial-mesenchymal transition via the Wnt/β-catenin signaling pathway. Oncology reports 37 28849076
2016 The K⁺-dependent GTPase Nug1 is implicated in the association of the helicase Dbp10 to the immature peptidyl transferase centre during ribosome maturation. Nucleic acids research 35 26823502
2014 Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1. BMC medical genetics 25 24886551
2020 Integrative analyses prioritize GNL3 as a risk gene for bipolar disorder. Molecular psychiatry 21 32826963
2016 Nucleostemin/GNL3 promotes nucleolar polyubiquitylation of p27kip1 to drive hepatocellular carcinoma progression. Cancer letters 18 27998760
2021 RNA binding protein GNL3 up-regulates IL24 and PTN to promote the development of osteoarthritis. Life sciences 15 33358901
2019 The oncogenic role of GNL3 in the progression and metastasis of osteosarcoma. Cancer management and research 15 30936750
2022 GNL3 is an evolutionarily conserved stem cell gene influencing cell proliferation, animal growth and regeneration in the hydrozoan Hydractinia. Open biology 14 36069077
2021 OTX015 Epi-Drug Exerts Antitumor Effects in Ovarian Cancer Cells by Blocking GNL3-Mediated Radioresistance Mechanisms: Cellular, Molecular and Computational Evidence. Cancers 13 33806232
2018 Common variants in the GNL3 contribute to the increasing risk of knee osteoarthritis in Han Chinese population. Scientific reports 9 29942097
2022 GNL3 Regulates SIRT1 Transcription and Promotes Hepatocellular Carcinoma Stem Cell-Like Features and Metastasis. Journal of oncology 8 35432540
2021 RNA-seq reveal RNA binding protein GNL3 as a key mediator in the development of psoriasis vulgaris by regulating the IL23/IL17 axis. Life sciences 8 34487784
2024 Knockdown of GNL3 inhibits LUAD cell growth by regulating Wnt-β-catenin pathway. Allergologia et immunopathologia 3 38970264
2023 The nucleolar protein GNL3 prevents resection of stalled replication forks. EMBO reports 3 37965896
2022 Common variants in GNL3 gene contributed the susceptibility of hand osteoarthritis in Han Chinese population. Scientific reports 3 36167888
2026 Integrative genomics establishes GNL3 as a pleiotropic hub and causal gene for osteoarthritis. Human genomics 0 41699659
2026 GNL3 Orchestrates AR Transcriptional Programs to Drive Castration-Resistant Prostate Cancer and Immune Evasion. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 0 41772945
2026 Enolase 2-mediated lactylation-dependent disruption of the GNL3-MDM2-p53 axis in age-related osteoarthritis. Cellular & molecular biology letters 0 42192505
2025 GNL3 SUMOylation is essential for DNA double-strand break repair by homologous recombination. bioRxiv : the preprint server for biology 0 41279596

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