Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome

Dionne, Ugo; Gingras, Anne‐Claude

doi:10.3389/fmolb.2022.852911

Cited by 20 publications

(22 citation statements)

References 145 publications

(185 reference statements)

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“…Peroxidase-based PDB also catalyzes labeling in minutes but utilizes hydrogen peroxide to create biotin phenol radicals, which may be toxic in living cells and modulates signal transduction events. In addition, covalent tagging of tyrosine residues by biotin phenol radicals makes the use of peroxidases less desirable in PDB studies involving posttranslational modifications ( 56 ). We saw a distinct interaction profile of EGFR on the cell surface versus intracellularly.…”

Section: Discussionmentioning

confidence: 99%

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

Al Mismar,

Samavarchi-Tehrani,

Seale

et al. 2023

Preprint

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Plasma membrane proteins are critical mediators of cell-cell and cell-environment interactions, pivotal in intracellular signal transmission vital for cellular functionality. Proximity-dependent biotinylation approaches such as BioID combined with mass spectrometry have begun illuminating the landscape of proximal protein interactions within intracellular compartments. However, their deployment in studies of the extracellular environment remains scarce. Here, we present extracellular TurboID (ecTurboID), a method designed to profile cell surface interactions in living cells on short timescales. We first report on the careful optimization of experimental and data analysis strategies that enable the capture of extracellular protein interaction information. Leveraging the ecTurboID technique, we unveiled the proximal interactome of multiple plasma membrane proteins, notably the epidermal growth factor receptor (EGFR). This led to identifying the low-density lipoprotein receptor (LDLR) as a newfound extracellular protein associating with EGFR, contingent upon the presence of the EGF ligand. We showed that 15 minutes of EGF stimulation induced LDLR localization to the plasma membrane to associate with proteins involved in EGFR regulation. This modified proximity labelling methodology allows us to dynamically study the associations between plasma membrane proteins in the extracellular environment.One Sentence SummaryWe developed extracellular TurboID (ecTurboID) as a new proximity dependent biotinylation approach that can capture dynamic interactions at the cell surface, identifying Low-Density Lipoprotein Receptor as a new ligand-dependent extracellular partner of Epidermal Growth Factor Receptor.

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Section: Discussionmentioning

confidence: 99%

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

Al Mismar,

Samavarchi-Tehrani,

Seale

et al. 2023

Preprint

Self Cite

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“…Most recently, in mammalian cells, using proximity-dependent biotin labeling (BioID) [ 94 ], mSIN1 was identified as one of the targets of oncogenic RAS mutants and the RBD of mSIN1 was required for RAS binding in pull-down assays [ 95 , 96 ]. Moreover, two groups have obtained crystal structures of the mSIN1 RBD in complex with K-RAS (4A isoform) [ 40 ] and/or H-RAS [ 41 ].…”

Section: Control Of Torc2 By Small Gtpasesmentioning

confidence: 99%

TOR complex 2 is a master regulator of plasma membrane homeostasis

Thorner

2022

Biochemical Journal

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As first demonstrated in budding yeast (Saccharomyces cerevisiae), all eukaryotic cells contain two, distinct multi-component protein kinase complexes that each harbor the TOR (Target Of Rapamycin) polypeptide as the catalytic subunit. These ensembles, dubbed TORC1 and TORC2, function as universal, centrally important sensors, integrators, and controllers of eukaryotic cell growth and homeostasis. TORC1, activated on the cytosolic surface of the lysosome (or, in yeast, on the cytosolic surface of the vacuole), has emerged as a primary nutrient sensor that promotes cellular biosynthesis and suppresses autophagy. TORC2, located primarily at the plasma membrane, plays a major role in maintaining the proper levels and bilayer distribution of all plasma membrane components (sphingolipids, glycerophospholipids, sterols, and integral membrane proteins). This article surveys what we have learned about signaling via the TORC2 complex, largely through studies conducted in S. cerevisiae. In this yeast, conditions that challenge plasma membrane integrity can, depending on the nature of the stress, stimulate or inhibit TORC2, resulting in, respectively, up-regulation or down-regulation of the phosphorylation and thus the activity of its essential downstream effector the AGC family protein kinase Ypk1. Through the ensuing effect on the efficiency with which Ypk1 phosphorylates multiple substrates that control diverse processes, membrane homeostasis is maintained. Thus, the major focus here is on TORC2, Ypk1, and the multifarious targets of Ypk1 and how the functions of these substrates are regulated by their Ypk1-mediated phosphorylation, with emphasis on recent advances in our understanding of these processes.

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“…Methods that highlight such interactions can provide key insights into basic molecular mechanisms and help target strategies for therapeutic interventions (1). One such method is proximity-dependent protein labeling, which can both characterize protein-protein interaction networks and define the proteomes of subcellular structures (1,2). The proximity labeling enzymes most widely used in living cells and organisms are currently engineered variants of the E. coli biotin ligase BirA, such as TurboID, the ascorbate peroxidase APEX and its derivatives, and horseradish peroxidase HRP (1)(2)(3).…”

Section: Introductionmentioning

confidence: 99%

“…One such method is proximity-dependent protein labeling, which can both characterize protein-protein interaction networks and define the proteomes of subcellular structures (1,2). The proximity labeling enzymes most widely used in living cells and organisms are currently engineered variants of the E. coli biotin ligase BirA, such as TurboID, the ascorbate peroxidase APEX and its derivatives, and horseradish peroxidase HRP (1)(2)(3). These enzymes all release activated biotin, which reacts with amine groups of exposed lysine residues in the vicinity (4)(5)(6).…”

Section: Introductionmentioning

confidence: 99%

Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans

Artan

Hartl²,

Chen³

et al. 2022

Journal of Biological Chemistry

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Proximity-Dependent Biotinylation Approaches to Explore the Dynamic Compartmentalized Proteome

Cited by 20 publications

References 145 publications

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

TOR complex 2 is a master regulator of plasma membrane homeostasis

Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans

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