Affinage

Showing TBRG4 — FASTKD4 is a alias.

TBRG4

FAST kinase domain-containing protein 4 · UniProt Q969Z0

Length
631 aa
Mass
70.7 kDa
Annotated
2026-06-10
12 papers in source corpus 8 papers cited in narrative 8 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

TBRG4 (FASTKD4) is a mitochondrial RNA-binding protein that controls the stability, processing, and translation of specific mitochondrially encoded mRNAs (PMID:28335001, PMID:39727163). It is required for the maturation and stability of ND3, ND5, and CYB transcripts, with its loss reducing mature mRNA levels and causing accumulation of the ND5-CYB precursor (PMID:28335001). Its activity depends on a C-terminal RAP domain bearing a conserved aspartate that constitutes a predicted endonuclease active site, whereas the upstream region dictates RNA target selection and mitochondrial localization; in double-knockout epistasis TBRG4 is epistatic to FASTKD1 in setting ND3 levels (PMID:28335001). The atomic-resolution crystal structure reveals a RAP domain and two FAST motifs forming a positively charged cavity resembling the VsrI endonuclease, and TBRG4 binds the canonical poly(A) tail of MT-ND3 mRNA to enable its polyadenylation, stability, and translation (PMID:39727163). Through this control of mitochondrial gene expression, TBRG4 maintains mitochondrial homeostasis and limits ROS production: its depletion provokes mitochondrial stress and elevated ROS that drives KSHV and EBV lytic reactivation from latency, an effect reversed by a ROS scavenger (PMID:36417478).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2017 High

    Established TBRG4/FASTKD4 as a sequence-specific regulator of mitochondrial mRNA stability and processing, defining the functional architecture of the protein.

    Evidence CRISPR disruption, double-knockout epistasis, RAP-domain active-site (aspartate) mutagenesis, and FASTK chimera domain-swap experiments

    PMID:28335001

    Open questions at the time
    • Endonucleolytic cleavage activity was predicted from a conserved aspartate but not demonstrated biochemically on a defined substrate
    • Mechanism by which the upstream region selects specific transcripts not resolved
    • Direct catalytic vs. scaffolding contribution of the RAP domain not distinguished
  2. 2022 Medium

    Connected TBRG4's mitochondrial function to a cellular phenotype, showing it suppresses ROS and thereby represses gammaherpesvirus lytic reactivation.

    Evidence shRNA/siRNA knockdown in latently infected cells with viral reactivation readouts, ROS measurement, and ROS-scavenger rescue

    PMID:36417478

    Open questions at the time
    • Link between specific mitochondrial mRNA defects and the ROS increase not mechanistically traced
    • Direct viral target genes of the ROS signal not identified
    • Mitochondrial localization inferred rather than rigorously demonstrated
  3. 2025 High

    Provided the structural and biochemical basis for TBRG4 function, showing direct poly(A)-tail binding of MT-ND3 mRNA couples to its maturation and translation.

    Evidence Atomic-resolution crystal structure, in vitro RNA-binding assays, and cell-based loss-of-function with MT-ND3 polyadenylation/stability readouts

    PMID:39727163

    Open questions at the time
    • Whether the VsrI-like cavity performs endonucleolytic cleavage on physiological substrates not shown
    • Structural basis of target discrimination among ND3/ND5/CYB not resolved
    • How poly(A) binding mechanistically enhances translation not defined
  4. 2020 Low

    Reported context-dependent tumor-promoting roles for TBRG4 in osteosarcoma and esophageal carcinoma, linking its loss to ROS-driven mitochondrial apoptosis.

    Evidence shRNA knockdown with proliferation/invasion/apoptosis assays, xenografts, CAV-1 overexpression rescue, and Western blot of PI3K/AKT and BCL-2/BAX/cytochrome c markers

    PMID:32240636 PMID:32415943

    Open questions at the time
    • Pathway placement (TGF-β1/PI3K-AKT, CAV-1) rests on knockdown plus Western blot without direct binding or reconstitution
    • Connection to TBRG4's mitochondrial RNA function not established
    • Single-lab findings per cancer type
  5. 2024 Low

    Implicated TBRG4 in autophagy and ferroptosis regulation through a physical interaction with Beclin1.

    Evidence Co-IP/mass spectrometry for Beclin1 interaction, Western blot for ubiquitination, and ROS/mitochondrial membrane potential and apoptosis assays in hepatocellular carcinoma and nucleus pulposus cells plus a rat IDD model

    PMID:38347489 PMID:40379025

    Open questions at the time
    • Beclin1 interaction shown by Co-IP/MS without reciprocal validation or mapping of the interaction interface
    • Reduced Beclin1 ubiquitination assessed by Western blot without identifying the responsible E3 ligase or reconstituting the pathway
    • DDX56/p-AKT/GSK3β placement lacks direct mechanistic follow-up
  6. 2025 Low

    Reported TBRG4 as an upstream activator of TGF-β/SMAD3 signaling driving EMT in pancreatic cancer.

    Evidence shRNA knockdown and overexpression with migration/invasion/EMT assays and pharmacological rescue (TGF-β1 agonist SRI-011381; receptor inhibitor SB431542) plus xenografts

    PMID:39821094

    Open questions at the time
    • Pathway placement is pharmacological and indirect, with no direct molecular interaction shown
    • How a mitochondrial RNA-binding protein activates cytoplasmic TGF-β/SMAD3 not explained
    • Single-lab study

Open questions

Synthesis pass · forward-looking unresolved questions
  • Whether the predicted RAP-domain endonuclease cleaves its mitochondrial mRNA substrates directly, and how the mitochondrial function mechanistically connects to the reported cytoplasmic signaling, autophagy, and ferroptosis phenotypes, remains unresolved.
  • No demonstrated in vitro endonucleolytic cleavage on a defined transcript
  • No mechanistic bridge between mitochondrial mRNA regulation and TGF-β/PI3K-AKT/Beclin1 phenotypes
  • Causal role for ROS established only pharmacologically in select contexts

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0140098 catalytic activity, acting on RNA 2
Localization
GO:0005739 mitochondrion 2
Pathway
R-HSA-8953854 Metabolism of RNA 2
Partners
BECN1

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 FASTKD4 (TBRG4) is required for the stability of specific mitochondrial mRNAs including ND3, ND5, and CYB; CRISPR-mediated disruption of FASTKD4 reduces levels of these mature mRNAs and causes accumulation of ND5-CYB precursor RNA. Disrupting both FASTKD1 and FASTKD4 results in decreased ND3 similar to FASTKD4 loss alone, indicating FASTKD4 is epistatic to FASTKD1. Mutation of a conserved aspartate residue in the RAP domain (predicted nuclease active site) abolishes FASTKD4 function. Chimera experiments show the RAP domain is essential for function while the upstream region determines RNA targeting and protein localization. CRISPR-mediated gene disruption, double-knockout epistasis analysis, active-site mutagenesis (aspartate substitution), FASTK chimera experiments, structural modeling of RAP domain nuclease fold Nucleic acids research High 28335001
2025 FASTKD4 (TBRG4) binds the canonical poly(A) tail of MT-ND3 mRNA to enable its maturation and translation. Loss of FASTKD4 in cells decreases MT-ND3 polyadenylation, destabilizing the messenger RNA. The crystal structure of FASTKD4 at atomic resolution reveals a RAP domain and two FAST motifs forming a positively charged cavity resembling the VsrI endonuclease, consistent with RNA-binding and processing activity. Crystal structure determination (atomic resolution), in vitro RNA-binding biochemical assays, cell-based loss-of-function with MT-ND3 polyadenylation and stability readout Nucleic acids research High 39727163
2022 TBRG4 is localized to the mitochondria and acts as a cellular repressor of KSHV and EBV lytic reactivation from latency. Knockdown of TBRG4 causes mitochondrial stress, increases reactive oxygen species (ROS) production, and induces viral lytic gene transcription and replication. Treatment with a ROS scavenger decreases viral reactivation in TBRG4-depleted cells, placing ROS downstream of TBRG4 in this pathway. Knockdown (shRNA/siRNA) in latently infected cells, viral lytic gene transcription and replication assays, ROS measurement, ROS scavenger rescue experiment, mitochondrial localization (implied by fractionation/imaging) PLoS pathogens Medium 36417478
2020 TBRG4 knockdown in osteosarcoma cells suppresses proliferation, invasion, and induces apoptosis in vitro and in vivo. Mechanistically, TBRG4 knockdown reduces TGF-β1 expression and inactivates the PI3K/AKT signaling pathway, as evidenced by decreased p-PI3K and p-AKT levels. Lentivirus-mediated shRNA knockdown, CCK8/high-content screening/flow cytometry/Transwell invasion assays, xenograft in vivo model, Western blot for p-PI3K, p-AKT Archives of biochemistry and biophysics Low 32240636
2020 In esophageal squamous cell carcinoma cells, TBRG4 knockdown reduces CAV-1 (caveolin-1) expression and promotes ROS formation and mitochondria-dependent apoptosis. CAV-1 overexpression in TBRG4-knockdown cells rescues TBRG4 expression, reduces ROS, and reverses cell-cycle arrest and apoptosis, placing CAV-1 downstream of TBRG4 in regulating intracellular ROS and the BCL-2/BAX/cytochrome c apoptotic pathway. shRNA knockdown of TBRG4 and/or CAV-1, CAV-1 overexpression rescue, ROS measurement, apoptosis (BCL-2/BAX/cytochrome c Western blot), cell-cycle analysis Cellular and molecular biology Low 32415943
2024 TBRG4 interacts with Beclin1 in hepatocellular carcinoma cells, as shown by co-immunoprecipitation. TBRG4 knockdown inhibits proliferation, migration, and invasion and acts through the DDX56/p-AKT/GSK3β signaling pathway. TBRG4 deficiency also reduces mitochondrial membrane potential and increases ROS, promoting ferroptosis. Co-immunoprecipitation (Co-IP), Western blot, RT-PCR, laser confocal microscopy, scratch/Transwell assays, ROS/mitochondrial membrane potential measurement BMC cancer Low 38347489
2025 TBRG4 interacts with Beclin1 and reduces its ubiquitination, thereby promoting autophagy. TBRG4 knockdown exacerbates mitochondrial dysfunction and increases apoptosis via the BCL2/caspase-3 pathway in nucleus pulposus cells. TBRG4 overexpression in vivo (rat IDD model) restores mitochondrial function and reduces disc degeneration. Co-immunoprecipitation and mass spectrometry to identify interacting proteins (Beclin1), Western blot for ubiquitination, autophagy/apoptosis assays (immunofluorescence, flow cytometry), rat IDD in vivo model The spine journal Low 40379025
2025 TBRG4 knockdown in pancreatic cancer cells inhibits migration, invasion, and EMT. TBRG4 activates TGF-β/SMAD3 signaling; a TGF-β1 agonist (SRI-011381) rescues the TBRG4-knockdown phenotype and a TGF-β type I receptor inhibitor (SB431542) reverses TBRG4 overexpression-driven invasion and EMT, placing TBRG4 upstream of TGF-β/SMAD3 in this context. shRNA knockdown, overexpression, wound-healing/Transwell assays, Western blot for EMT markers and SMAD3 phosphorylation, pharmacological rescue (SRI-011381 agonist; SB431542 inhibitor), xenograft mouse model Histology and histopathology Low 39821094

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain. Nucleic acids research 49 28335001
2023 High expression of novel biomarker TBRG4 promotes the progression and invasion of oral squamous cell carcinoma. Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology 19 37537882
2020 Knockdown of TBRG4 suppresses proliferation, invasion and promotes apoptosis of osteosarcoma cells by downregulating TGF-β1 expression and PI3K/AKT signaling pathway. Archives of biochemistry and biophysics 18 32240636
2017 Knockdown of TBRG4 affects tumorigenesis in human H1299 lung cancer cells by regulating DDIT3, CAV1 and RRM2. Oncology letters 15 29387213
2024 High expression of TBRG4 in relation to unfavorable outcome and cell ferroptosis in hepatocellular carcinoma. BMC cancer 11 38347489
2022 Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency. PLoS pathogens 11 36417478
2020 TBRG4 silencing promotes progression of squamous cell carcinoma via regulation of CAV-1 expression and ROS formation. Cellular and molecular biology (Noisy-le-Grand, France) 8 32415943
2020 TBRG4 Knockdown Suppresses Proliferation and Growth of Human Osteosarcoma Cell Lines MG63 Through PI3K/Akt Pathway. OncoTargets and therapy 8 32801755
2025 The Vsr-like protein FASTKD4 regulates the stability and polyadenylation of the MT-ND3 mRNA. Nucleic acids research 6 39727163
2025 Knockdown of TBRG4 suppresses the migration, invasion, and epithelial-to-mesenchymal transition of pancreatic cancer cells via TGF-β/smad3 signaling. Histology and histopathology 4 39821094
2010 Assessment of constitutive activity of a G protein-coupled receptor, CPR2, in Cryptococcus neoformans by heterologous and homologous methods. Methods in enzymology 3 21036243
2025 TBRG4 regulates ubiquitination of Beclin1 and participates in autophagy pathway to inhibit intervertebral disc degeneration. The spine journal : official journal of the North American Spine Society 0 40379025

Missed literature

Know a paper Affinage missed for TBRG4? Flag it for the maintainers and the community.

No submissions yet.