Team Director
Satoko Arakawa
Ph.D.
Laboratory for Ultrastructural Research
LocationKobe / Developmental Biology Buildings
E-mailarako@riken.jp
The Laboratory for Ultrastructural Research aims to elucidate the relationship between cellular structure and function, using electron microscopy–based ultrastructural analysis as a central approach. Intracellular architecture changes dynamically in response to genetic variation, cell–cell interactions, and environmental cues, and its disruption can lead to functional abnormalities and pathophysiological states in living tissues.
We seek to understand how structural changes shape cellular and tissue function through studies of morphological transitions during differentiation, the physiological role of Golgi membrane-associated degradation (GOMED), and previously uncharacterized forms of cell death in tissues.
Selected Publications
Nibe-Shirakihara Y, Honda S, Arakawa S, et al.
Optineurin is an adaptor protein for ubiquitinated substrates in Golgi membrane-associated degradation.
Nature Communications
16, 8966 (2025)
doi: 10.1038/s41467-025-64400-3
Yamaguchi H, Honda S, Torii S, et al.
Wipi3 is essential for alternative autophagy and its loss causes neurodegeneration
Nature Communications
11, 5311 (2020)
doi: 10.1038/s41467-020-18892-w
Torii S, Yamaguchi H, Nakanishi A, et al.
Identification of a phosphorylation site on Ulk1 required for genotoxic stress-induced alternative autophagy
Nature Communications
11, 1754 (2020)
doi: 10.1038/s41467-020-15577-2
Arakawa S, Tsujioka M, Yoshida T, et al.
Role of Atg5-dependent cell death in the embryonic development of Bax/Bak double-knockout mice
Cell Death & Differentiation
24(9), 1598-1608 (2017)
doi: 10.1038/cdd.2017.84
Watanabe Y, Honda S, Konishi A, et al.
Autophagy controls centrosome number by degrading Cep63
Nature Communications
7, 13508 (2016)
doi: 10.1038/ncomms13508
Yamaguchi H, Arakawa S, Kanaseki T, et al.
Golgi membrane-associated degradation pathway in yeast and mammals
The EMBO Journal
35(18), 1991-2007 (2016)
doi: 10.15252/embj.201593191
Honda S, Arakawa S, Nishida Y, et al.
Ulk1-mediated Atg5-independent macroautophagy mediates elimination of mitochondria from embryonic reticulocytes
Nature Communications
5, 4004 (2014)
doi: 10.1038/ncomms5004
Narita M, Young A, Arakawa S, et al.
Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes
Science
332(6032), 966-970 (2011)
doi: 10.1126/science.1205407
Nishida Y, Arakawa S, Fujitani K, et al.
Discovery of Atg5/Atg7-independent alternative macroautophagy
Nature
461(7264), 654-658 (2009)
doi: 10.1038/nature08455
Shimizu S, Kanaseki T, Mizushima N, et al.
Role of Bcl-2 family proteins in a non-apoptotic programmed cell death dependent on autophagy genes
Nature Cell Biology
6(12), 1221-1228 (2004)
doi: 10.1038/ncb1192