Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

Abstract

Proteins perform biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches such as phage display, yeast hybridization, etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity-dependent labeling (PDL) of interacting proteins has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently. Among the PDL methods, BioID is the earliest and the most widely used one and has been upgraded from its prototype, making it an extremely convenient research tool. In this review, we describe the BioID technology development, its potential applications according to the nature of the target protein, and some recent efforts to circumvent the technical limitations. Moreover, some comparable PDL methods are introduced, including selective proteomic proximity labeling assay using tyramide, enzyme-mediated activation of radical sources, Proximity Labeling with Ascorbate Peroxidase, in vivo proximal labeling, etc., and we propose that systematic comparison of the working radius of these methods may be helpful to develop a tool box, from which the right method can be selected for a given target protein for PPI research.

Post-translational regulation of plant immunity

“…Although phosphorylation is a prominent posttranslational mechanism for propagating rapid and transient immune responses, identifying the kinases upstream of a known substrate remains a major challenge. The use of targeted, quantitative proteomics and the application of proximity-dependent affinity labeling of protein complexes in vivo show promise for the discovery of unknown kinases [62,63••,64••]. Additionally, advances in the sensitivity of proteomics instrumentation is rapidly increasing our ability to detect PTMs that occur in low stoichiometry, and therefore will open the door to understanding how these modifications contribute to immune responses.…”

Towards improving proximity labeling by the biotin ligase BirA

“…In recent years, methods that provide a snapshot of protein-protein interactions in the cell have been developed. Proximity-dependent labeling techniques utilize enzymes fused to a protein of interest (POI) that can transfer a molecular tag to proteins situated within a suitable labeling radius in the cell [1][2][3]. The molecular tag facilitates enrichment and identification of the labeled species, the latter usually by mass spectrometry (MS).…”

Alternative proteins are functional regulators in cell reprogramming by PKA activation

“…MS-based proteomic strategies are particularly well suited for measuring PPIs at a larger scale from a limited amount of complex mixture ( 17 ). This includes affinity purification ( 18 ) and tandem affinity purification ( 19 , 20 ), proximity labelling ( 21 ) such as APEX ( 22 ) and BioID ( 23–25 ), viral particle sorting approach (Virotrap) ( 26 ) and cross-linking mass spectrometry (XL-MS) ( 27 , 28 ). XL-MS is based on the formation of covalent bonds using a chemical linker of a defined length to freeze the interaction between partners.…”