A proximity labeling protocol to probe proximity interactions in C. elegans

Sanchez, Ariana D.; Feldman, Jessica L.

doi:10.1016/j.xpro.2021.100986

Cited by 10 publications

(8 citation statements)

References 10 publications

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“…TurboID was found to provide tissue- and region-specific promiscuous biotinylation in Caenorhabditis elegans . Additionally by studying non-centromeric microtubule organizing centers (ncMTOCs) in intestinal cells, it was demonstrated that its tissue-specific and region-specific proximity markers make it suitable for in vivo targeted protein network analysis [ 133 ]. Artan et al optimized the proximity labeling approach using TurboID for Caenorhabditis elegans .…”

Section: Applications Of Biotin Ligase-based Proximity Marker Technologymentioning

confidence: 99%

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Guo,

et al. 2023

Cell Commun Signal

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Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms.

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Section: Applications Of Biotin Ligase-based Proximity Marker Technologymentioning

confidence: 99%

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Guo,

et al. 2023

Cell Commun Signal

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“…Proteomics based on proximity-labeling strategies using biotin ligases ( e.g. , BioID, TurboID-NES) are being increasingly used in in vitro and in vivo experimental contexts and in model systems ranging from plants ( 17 , 64 , 65 , 66 ), yeast ( 67 ), zebrafish ( 68 , 69 ), Drosophila ( 70 , 71 ), Caenorhabditis elegans ( 16 , 72 ), to mouse models ( 18 , 21 , 22 , 73 ). TurboID is one of the most efficient biotin ligases that can effectively label several proteins within a 10 nm labeling radius in mammalian cells.…”

Section: Discussionmentioning

confidence: 99%

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Sunna¹,

Bowen²,

Zeng³

et al. 2023

Molecular & Cellular Proteomics

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“…Proteomics based on proximity-labeling strategies using biotin ligases (e.g. BioID, TurboID-NES) are being increasingly used in in vitro and in vivo experimental contexts and in model systems ranging from plants 17,[51][52][53] , yeast 54 , zebrafish 55,56 , Drosophila 57,58 , C. elegans 16,59 , to mouse models 18,21,22,60 . TurboID is one of the most efficient biotin ligases that can effectively label several proteins within a 10nm labeling radius in mammalian cells.…”

Section: Discussionmentioning

confidence: 99%

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

Sunna

Bowen

Zeng

et al. 2022

Preprint

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Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level, can provide biological and therapeutic insights. Conventional approaches to investigate cell type-specific proteomes from brain are incompatible with the survival of adult murine neurons and contamination from non-target cell-types and experimental artifacts confound the data. To overcome these barriers, in vivo proteomic labeling with proximity dependent biotinylation of cytosolic proteins using TurboID with a Nuclear Export Sequence (TurboID-NES), coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy to sample cell type-specific proteomes in the native state of cells without need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID-NES approach are representative of the whole cell proteome, and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing TurboID-NES to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-NES expression and biotinylation did not significantly impact homeostatic cellular proteomes of BV2 and N2A cells, and did not affect cytokine production or mitochondrial respiration of BV2 cells under resting or lipopolysaccharide (LPS)-stimulated conditions. TurboID-NES mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. Acute LPS treatment significantly altered microglial proteomes, but not N2A proteomes. LPS treatment induced >500 differentially expressed proteins in transduced BV2 proteomes, including an increase in canonical M1 proteins (IL1a, Irg1, Oasl1) and a decrease in canonical M2 proteins (Arg1, MGl2).

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A proximity labeling protocol to probe proximity interactions in C. elegans

Cited by 10 publications

References 10 publications

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

The development of proximity labeling technology and its applications in mammals, plants, and microorganisms

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

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