Medical Sciences Group/Intra-University Cooperative LaboratoriesSaeki Laboratory
(Divisionof Protein Metabolism, IMS)

The ubiquitin-proteasome system (UPS) is a major protein degradation system that regulates virtually all cellular functions in eukaryotic cells. Since the maintenance of proteostasis is essential for human health, UPS dysfunction causes various diseases including cancer, inflammation, and neurodegeneration. Therefore, the UPS regulators are attractive targets for drug discovery, and indeed, the development of proteasome inhibitors and protein degraders such as PROTACs has been rapidly expanding. However, much of the molecular mechanisms underlying the UPS remain elusive due to their complexity, and tools for accurate estimation of UPS function are limited. Our goal is to elucidate the fundamental mechanisms of ubiquitin signaling and proteasomal degradation to understand pathophysiology and to develop therapeutic strategies for UPS-related diseases.

Ubiquitin-proteasome system, Proteostasis, Neural stem cells, Liquid-liquid phase separation, Mass spectrometry
Elucidation of the molecular mechanisms underlying the ubiquitin-proteasome system

Previously, it was simply thought that ubiquitylated proteins are directly recognized and degraded by the proteasome. However, we found that the ubiquitin-selective chaperone p97 ATPase and the UBL-UBA proteins play a crucial role in the selection and delivery of proteasome substrates to the proteasome (Mol Cell 2017; Nat Commun 2018, 2019). We also found that branched ubiquitin chains enhance proteasomal degradation of several substrate proteins (PNAS 2018, Mol Cell 2021). Because multiple proteasome-interacting proteins regulate proteasome activity, proteasomal degradation would be finely regulated at various levels. To elucidate the molecular mechanisms behind efficient proteasomal degradation, we are investigating the high-order structure of ubiquitin chains, the substrate selectivity of ubiquitin-binding proteins, and protein lifetime analysis using deep proteomics and novel chemical tools.

  • Ubiquitin-proteasome system (UPS) and diseases

Biological significance of proteasome phase separation

Proteasomes are diffusely localized in the cytoplasm and nucleoplasm, but, we recently found that hyperosmotic stress induces the ubiquitin-dependent liquid-liquid phase separation (LLPS) of the proteasome, which forms proteolytic droplets in the nucleus (Nature 2020). As this LLPS could be associated with the ubiquitin-positive inclusion bodies observed in various neurodegenerative diseases, we are further investigating whether various stresses induce proteasome droplets.

  • Ubiquitin-dependent phase separation of the proteasome

Analysis of proteasome mutant mice

The proteasome plays a central role in maintaining proteostasis, but research at the individual level has lagged far behind. We have generated systemic proteasome mutant mice based on recently identified gene mutations in patients. By analyzing the phenotypes of these mice, we aim to understand the pathophysiological mechanism of the proteasome-related diseases, "proteasomopathies".

Proteostasis in adult neural stem cells

Neural stem cells in the adult brain produce new neurons throughout life and contribute to various brain functions such as memory and learning. However, most adult neural stem cells are maintained in a quiescent (dormant) state, neither proliferating nor differentiating. Our group is interested in the molecular mechanisms that regulate the quiescence of neural stem cells in brain tissue, focusing on the remodeling in the maintenance and disruption of protein homeostasis (proteostasis). We have revealed that lysosomes, which are intracellular organelles responsible for final degradation, regulate the maintenance of neural stem cell quiescence and that proteolytic activity by lysosomes fluctuates significantly associated with aging and brain diseases (Nat Commun 2019, and others).

  • Molecular mechanisms maintaining the quiescent state of neural stem cells

  • 1. Endo et al. USP8 prevents aberrant NF-κB and Nrf2 activation by counteracting ubiquitin signals from endosomes. J Cell Biol in press
  • 2. Kaiho-Soma et al. TRIP12 promotes small-molecule-induced degradation through K29/K48-branched ubiquitin chains. Mol Cell 81, 1411-1424.e7 (2021)
  • 3. Yasuda, Tsuchiya, Kaiho, et al. Stress- and ubiquitylation-dependent phase separation of the proteasome. Nature 578, 296-300 (2020)
  • 4. Sato, Tsuchiya, et al. Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Nat Commun 10, 5708 (2019)
  • 5. Kobayashi et al. Enhanced lysosomal degradation maintains the quiescent state of neural stem cells. Nat Commun 10, 5446 (2019)
  • 6. Tsuchiya, Burana, et al. Ub-ProT reveals global length and composition of protein ubiquitylation in cells. Nat Commun 9, 524 (2018)
  • 7. Tsuchiya et al. In vivo ubiquitin linkage-type analysis reveals that the Cdc48-Rad23/Dsk2 axis contributes to K48-linked chain specificity of the proteasome. Mol Cell 66, 488-502 (2017)

We are looking for students who are passionate about life science research and highly motivated to become creative researchers. There is a journal club/progress report in English once a week and an individual research discussion with his/her supervisor once a week. We hope that our students will first learn scientific thinking and then grow into world-class researchers. Laboratory tours are welcome at any time.

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