RIKEN Center for Biosystems Dynamics Research Laboratory for Ultrastructural Research

Team Director: Satoko Arakawa (Ph.D.)

Japanese Page

Research Summary

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 dynamically changes 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.

Main Research Fields

Biology

Related Research Fields

Medicine, Dentistry & Pharmacy
Morphology and anatomical structure-related
Cell biology-related
Experimental pathology-related

Keywords

Ultrastructural analysis
Correlative light and electron microscopy (CLEM)
Cell death, autophagy, and GOMED
Organelle remodeling
Hematopoietic differentiation

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

1.* 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).
2.* Yamaguchi H, Honda S, Torii S. et al.
Wipi3 is essential for alternative autophagy and its loss causes neurodegeneration"
Nature Communications 11(1):5311 (2020).
3.* 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(1):1754 (2020).
4.* 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).
5.* Watanabe Y, Honda S, Konishi A, et al.
"Autophagy controls centrosome number by degrading Cep63"
Nature Communications 7:13508 (2016).
6.* 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).
7.* 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).
8.* Narita M, Young AR, Arakawa S, et al.
"Spatial coupling of mTOR and autophagy augments secretory phenotypes"
Science 332(6032):966-70 (2011).
9.* Nishida Y, Arakawa S, Fujitani K,et al.
"Discovery of Atg5/Atg7-independent alternative macroautophagy"
Nature 461(7264): 654-658 (2009).
10.* 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)

Lab Members

Principal investigator

Satoko Arakawa: Team Director

Contact Information

2-2-3 Minatojima-minamimachi, Chuo-ku
Kobe, Hyogo
650-0047 Japan
Email: arako@riken.jp