Proximity labeling strategies in Caenorhabditis elegans: a comprehensive review.

The field of proteomics has been revolutionized by the development of proximity labeling (PL), a method that allows for the in vivo mapping of protein-protein interactions (PPIs) and the characterization of regulated proteomes. In the model organism C. elegans, PL methods offer new opportunities to unravel spatially and temporally regulated protein networks. This review offers a comprehensive overview of the principles and applications of PL strategies, including peroxidase-based (APX) and biotin ligase-based (BioID, TurboID, miniTurboID, and UltraID) systems, as applied in C. elegans research. We highlight how these tools address the limitations of traditional interactomics methods such as co-immunoprecipitation and yeast two-hybrid, enabling the study of transient, weak, and compartment-specific protein networks. Furthermore, we discuss recent innovations, such as nanobody-based indirect labeling, which expand the versatility and precision of PL. We also discuss the practical considerations, technical challenges, and future directions for advancing PL technology in C. elegans to build a more holistic understanding of protein function within a living organism. Collectively, these developments establish PL as a robust framework for dissecting dynamic proteomic interactions within the physiological context of C. elegans.