Proteome Homeostasis Research Unit

Our unit aims to reveal how the protein homeostasis (“proteostasis”) is regulated and maintained at the system level. To this end, we develop cutting-edge proteomic technologies to capture protein-specific information, including translation, degradation, post-translational modifications, activity, and protein-protein interactions. Lipids regulate proteostasis through binding covalently or non-covalently to proteins. We previously developed a proteomic methodology for global analysis of endogenous protein N-terminal myristoylation sites based on liquid-liquid extraction of hydrophobic lipidated peptides (Tsumagari et al., Mol. Cell. Proteomics 2023). In FY2025, we have developed new methods for more global, site-resolved analysis of multiple protein lipidations, including myristoylation, palmitoylation and prenylation. (Tsumagari et al., submitted 2026). Using these approaches, we revealed that palmitoylation of a ribosomal protein influences nuclear export of pre-40S ribosomal subunits. These findings suggest a regulatory role for S-acylation in ribosome biology, offering new insights into the modulation of translation machinery through lipid modifications. In addition, we studied and focused on mapping the repertoire of surface proteins and interacting proteins of extracellular vesicles (EVs), which provide deeper insight into their biological, diagnostic, and therapeutic roles. To do this, we developed a genetically encoded proximity labelling probe that displays engineered ascorbate peroxidase, APEX2, on the surface of EVs via fusion to EV-sorting scaffold proteins (Fig) (Zheng et al., Adv. Sci. 2025). This enables the biotinylation of producer-cell-derived surface proteins, corona proteins, and interactors in vitro. After the enrichment by streptavidin bead pulldowns, subpopulation-specific, biotinylated surfaceome and interactome are comprehensively characterized using mass spectrometry-based proteomics. Thus, a genetic tool is introduced for the high-fidelity mapping of the surfaceome and cellular interactome of EVs in vitro. This approach offers a robust framework for dissecting EV biology and has broad applications in biomarker discovery and EV-based therapeutics.