In vivo interactome profiling by enzyme‐catalyzed proximity labeling

Abstract

Enzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the protein-protein interaction networks, dissect complex biological processes, and characterize the subcellular proteome in a more physiological setting than before. The enzymatic tags are being upgraded to improve temporal and spatial resolution and obtain faster catalytic dynamics and higher catalytic efficiency. In vivo application of PL integrated with other state of the art techniques has recently been adapted in live animals and plants, allowing questions to be addressed that were previously inaccessible. It is timely to summarize the current state of PL-dependent interactome studies and their potential applications. We will focus on in vivo uses of newer versions of PL and highlight critical considerations for successful in vivo PL experiments that will provide novel insights into the protein interactome in the context of human diseases.

Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling

“…Proximity-labeling methods overcome many of these limitations (1, [6][7][8], and have allowed the proteomes of subcellular compartments (1), and weak or transient PPIs to be characterized in vivo (1). Proximity labeling fuses a protein of interest to an enzyme domain that promiscuously tags proteins in its vicinity with a biochemical handle.…”

Interactome analysis ofC. eleganssynapses by TurboID-based proximity labeling

“…However, each method has limitations that can include high false positive rates, poor detection of transient or weak interactors, a low signal-to-noise ratio when detecting PPIs in specific cell types or subcellular compartments, artefacts created during tissue homogenization, and competing requirements for solubilizing proteins while keeping complexes intact ( 1, 2 ). Proximity-labeling methods overcome many of these limitations ( 1, 6–8 ), and have allowed the proteomes of subcellular compartments ( 1 ), and weak or transient PPIs to be characterized in vivo ( 1 ). Proximity labeling fuses a protein of interest to an enzyme domain that promiscuously tags proteins in its vicinity with a biochemical handle.…”

Disease‐specific interactome alterations via epichaperomics: the case for Alzheimer’s disease

“…APEX uses engineered ascorbic acid peroxidase, which, following addition of H 2 O 2 , oxidizes phenol derivatives to biotin-phenoxyl radicals that covalently react with electron-rich amino acids [46]. Important biological information from the use of these methods has been derived, and excellent review articles provide an overview of such achievements [42,43,47,48].…”