Uncovering the In Vivo Proxisome Using Proximity-Tagging Methods

The development of new approaches is critical to gain further insights into biological processes that cannot be obtained by existing methods or technologies. The detection of protein-protein interaction is often challenging, especially for weak and transient interactions or for membrane proteins. Over the last decade, several proximity-tagging methodologies have been developed to explore protein interactions in living cells. Among those, the most efficient are based on protein partner modification, such as biotinylation or pupylation. Such technologies are based on engineered variants of enzymes like peroxidases or ligases that release reactive molecules, in the presence of specific substrates, that bind surrounding proteins. Fusing a protein of interest (POI) to these enzymes allows the definition of an unbiased proxisome, that is, all of the proteins in interaction or in close vicinity of the POI. Here, the different proximity-labeling tools available are described and comprehensive comparison to discuss advantages and limitations is provided.