TurboID-TRIM E3 ligases protome identification in U2OS cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Peiguo Yang
PROVIDER: PXD063270 | iProX | Thu Apr 24 00:00:00 BST 2025
REPOSITORIES: iProX
Similar Datasets
Project description:Identifiy G3BP1 interactome via TurboID labeling in mock or SFV infected U2OS cells
2025-03-10 | PXD061675 |
Project description:Identifiy G3BP1 interactome via TurboID labeling in mock or SFV infected U2OS cells
2025-03-10 | PXD061635 |
Project description:Biomolecular condensates, such as germ granules, organize RNA pathways critical for fertility and genome regulation. Yet, the protein composition and functional specialization of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that are required for fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors required for amplification of WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has co-evolved with PRG-1 across nematodes, with a conserved structured N-terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily co-adapted PIWI interactor critical for siRNA biogenesis.
2026-01-27 | GSE317407 | GEO
Project description:In this project, we used proximity labeling with TurboID to identify proteins that interact with DCAF15 in the presence of indisulam in a gastric cancer AGS cell line.
2021-08-26 | PXD024168 | Pride
Project description:Proximity labeling (PL) was recently developed to detect protein–protein interactions (PPIs) and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ligase, to a protein of interest (bait protein) to biotinylate adjacent proteins. The biotinylated protein can be purified by strep-tavidin beads, and identified by mass spectrometry (MS). TurboID is an engineered biotin ligase with high catalytic efficiency, which is used for proximity labeling. Although TurboID-based proximity labeling technology has been successfully established in mammals, its application in plant systems is limited. Here, we report the usage of TurboID for proximity labeling of FIP37, a core member of m6A methyltransferase complex, to identify FIP37 interacting proteins in Ara-bidopsis thaliana. By analyzing the MS data, we found 214 proteins biotinylated by GFP-TurboID-FIP37 fusion, including five components of m6A methyltransferase complex that have been previously confirmed. Therefore, the identified proteins may include potential proteins directly involved in the m6A pathway or functionally related to m6A-coupled mRNA processing due to spatial proximity. Moreover, we demonstrated the feasibility of proximity labeling tech-nology in plant epitranscriptomics studies, thereby expanding the application of this technology to more subjects of plant research.
2024-01-26 | PXD043041 | Pride
Project description:This study developed an integrated MCP-MS2/TurboID proximity labeling system to identify pre-miRNA156a-interacting proteins in vitro. By co-expressing MS2-tagged pre-miRNA156a with MCP-TurboID fusion protein, we achieved specific recruitment of TurboID to the target RNA. Following a 10-minute biotin pulse, proximal proteins were biotinylated, enriched using streptavidin magnetic beads, and separated by SDS-PAGE. Comparative analysis of differential protein bands between experimental and control groups, followed by LC-MS/MS analysis of excised gel bands (35-55 kDa), enabled systematic identification of pre-miRNA156a-binding proteins. This approach combines the specificity of MCP-MS2 interaction with the sensitivity of TurboID-mediated proximity labeling for comprehensive RNA-protein interactome profiling.
2025-07-15 | PXD066141 |
Project description:Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. Using the highly active biotin ligase TurboID, we optimize a proximity labeling protocol for C. elegans. We use this protocol to characterise the proteomes of the worm’s gut, muscle, skin, and nervous system. We express TurboID exclusively in the pair of AFD neurons and show we can identify known and previously unknown proteins expressed selectively in AFD. We knock TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identify many known ELKS-1 interacting proteins as well as previously uncharacterised synaptic proteins. Versatile vectors, and the inherent advantage of C. elegans for biochemistry, make proximity labeling a valuable addition to the nematode’s armory.
2021-09-15 | PXD027068 | Pride
Project description:It is documented that intracellular succinate levels are maintained and regulated by mitochondrial complexes II. In order to define the LONP1-dependent regulators of succinate content, unbiased TurboID-based proximity labeling was employed to exploit LONP1-targeting proteins. Our results showed that 63.5% of the proteins identified by LONP1-N-TurboID-based proximity labeling are mitochondrial proteins. Functional protein association networks analysis of the identified proteins indicated that these biotinylated proteins are related to carboxylic acid metabolic process, mitochondrial organization and mitochondrial gene expression.
2023-04-08 | PXD031197 | Pride
Project description:Proximity labeling has emerged as a prominent, reliable tool for obtaining local proteomes from a wide range of cell-types. Two major classes of labeling reagents, peroxidase based (APEX family), or biotin-ligase based (BioID family) have been developed in parallel. These two approaches are often used interchangeably, or chosen based on availability of reagents, however each may produce a biased proteome which should be considered during experimental design. We compared proximity labeling with TurboID or APEX2 in HEK293 cells across cytosol, nucleus, and membrane compartments. Both enzymes enriched compartment-specific proteomes, validated by GO terms, but showed distinct protein profiles. TurboID identified more membrane proteins, favoring identification of proteins associated with RNA processing and protein localization, while APEX2 enriched for proteins involved in metabolic pathways. Trypsin digestion highlighted biases from TurboID’s lysine biotinylation, which we show can be mitigated by an endoproteinase GluC digestion during sample prep, yet these differences persist to some degree. We find that TurboID suits broader proteomic studies whereas APEX2 targets specific signaling pathways. We therefore show that strategic enzyme and protease selection is critical for optimizing proximity labeling-based proteomic studies, advancing cellular proteome mapping.
2025-12-15 | PXD068036 | Pride
Project description:Analysis of U2AF2-TurboID-HA interactions by immunoprecipitation for comparison with proximity labeling. Cells expressing U2AF2 (iU2) fused with TurboID in either the undifferentiated state (D0) or after mesoderm differentiation (D1) were analyzed to identify the interactome and detect changes during the differentiation process.
2025-04-13 | PXD062890 | Pride