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Biomolecular Networks Laboratories

Laboratory of Mitochondrial Dynamics

Assoc. Prof. OKAMOTO Koji Assoc. Prof. OKAMOTO Koji

Keywords:

Yeast, Mitochondria, Organelle, Mitophagy

Unraveling mitochondrial quality and quantity control mechanisms

Mitochondria are energy-converting organelles that act as "the power plants of the cell", and change their quantity in response to cellular energy demand. They also accumulate oxidative stress from reactive oxygen species generated during electron transport, and damaged mitochondria are selectively eliminated from the cytoplasm. These quality and quantity control systems involve mitochondria-specific autophagy (mitophagy), and numerous studies suggest that defects in these systems are associated with various human diseases. Mitophagy is a catabolic process conserved from yeast to humans that sequesters and degrades mitochondria as whole organelles. The aim of our study is to uncover the general principle of mitophagy at the molecular and cellular levels, and elucidate the physiological function of this degradation process as an intracellular quality and quantity control system.

Custom-built photothermal microscopy (PTM)(left panel): Chromophore in mitochondria absorbs the pump laser energy and generates heat (only a few K). The refractive index around chromophore changes with heat. Variation in the refractive index induces deflection of the probe laser. Finally, the magnitude of probe laser deflection can be converted to optical signals, thereby visualizing mitochondria.
Label-free photothermal imaging of budding yeast (right panel): Using PTM, signals derived from intact mitochondria and vacuoles (lysosomal organelles) containing mitochondria delivered via mitophagy are seen in wild-type cells. The latter signal cannot be detected in cells lacking Atg32, a protein essential for mitophagy (atg32∆)

Members

Koji Okamoto (Associate Professor) okamoto.koji.fbs[at]osaka-u.ac.jp
Duan Lan(D3) dll[at]fbs.osaka-u.ac.jp
Mitsutaka Kubota(D3) kubota98[at]fbs.osaka-u.ac.jp
Yuki Nakayama(D2) yuki168[at]fbs.osaka-u.ac.jp
Sayaka Nagano(M2) u287877f[at]ecs.osaka-u.ac.jp    
Peijin Li(M1) lipeijin2[at]fbs.osaka-u.ac.jp
Rio Sato(M1) u186686d[at]ecs.osaka-u.ac.jp
Qiao Liu(research student) u060595i[at]ecs.osaka-u.ac.jp
Yuko Imada (Secretary) imada-yuu[at]office.osaka-u.ac.jp

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Q&A

What is your hot research topic?
Previous studies suggest that mitochondria are established independently from other organelles. However, it has recently become evident that they cooperate physically and functionally with other organelles such as the endoplasmic reticulum (ER), peroxisome, and lysosome. We found that selective degradation of mitochondria is also regulated via ER-localized proteins, and are now analyzing its molecular mechanisms.
What is your breakthrough or research progress in the last 5 years?
We have revealed that selective degradation of mitochondria is intimately linked to diverse processes including phospholipid methylation, protein N-terminal acetylation, phospholipid dephospholylation, nutrient/stress signaling, ER-associated degradation, and ER membrane protein insertion.
What kind of background do your lab members have?
The lab members have expertise in molecular biology, biochemistry, genetics, and cell biology using bacteria, yeast, and mammalian cultured cells as model systems.
Do you collaborate with other institutions and universities?
We are currently collaborating with researchers from Wakayama University, Nagoya City University, Johns Hopkins University (Baltimore, MA, USA), and the University of Groningen (Groningen, Netherlands).
What kind of careers do your Lab's alumni go on to?
Nine former lab members are now working at companies, two are taking a postdoc in Germany, and another is studying at a graduate school in the USA.
How do you develop your research?
We decipher basic principles underlying selective degradation of mitochondria at the molecular level in depth. Recently, using yeast, we have established a label-free method to detect selective degradation of mitochondria. We aim to elucidate the universality and diversity of selective mitochondrial degradation by making this method available to a variety of organisms other than model organisms used in the laboratory.

Research Highlights

Publications (Research Articles, Reviews, Books)

2021

Mitsutaka Kubota, Koji Okamoto

The protein N-terminal acetyltransferase A complex contributes to yeast mitophagy via promoting expression and phosphorylation of Atg32

J. Biochem. 170(2):175-182  2021 PMID:34115119 DOI:10.1093/jb/mvab068

Lan Duan, Koji Okamoto

Mitochondrial dynamics and degradation in the oleaginous yeast Lipomyces starkeyi

Genes Cells 26(8):627-635  2021 PMID:34085353 DOI:10.1111/gtc.12875

2020

Calvellia H, Krigman J, Onishi M, Narendra DP, Sun N, Okamoto K.

Detection of mitophagy in mammalian cells, mice, and yeast.

Methods Cell Biol. 155: 557-579  2020 PMID:32183977 DOI:10.1016/bs.mcb.2019.10.006

2019

Morita K, Matsuda F, Okamoto K, Ishii J, Kondo A, Shimizu H.

Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae.

Microb. Cell. Fact. 0.872916667  2019 PMID:31615527 DOI:10.1186/s12934-019-1226-6

Zheng L, Shu WJ, Li YM, Mari M, Yan C, Wang D, Yin ZH, Jiang W, Zhou Y,_Okamoto K, Reggiori F, Klionsky DJ, Song Z, Du HN.

The Paf1 complex transcriptionally regulates the mitochondrial-anchored protein Atg32 leading to activation of_mitophagy.

Autophagy 1月14日  2019 PMID:31525119 DOI:10.1080/15548627.2019.1668228

Murakawa T, Okamoto K, Omiya S, Taneike M, Yamaguchi O, Otsu K

A Mammalian Mitophagy Receptor, Bcl2-L-13, Recruits the ULK1 Complex to Induce Mitophagy.

Cell Reports 26: 338-345.e6  2019 PMID:30625316 DOI:10.1016/j.celrep.2018.12.050

2018

Yamada T, Murata D, Adachi Y, Itoh K, Kameoka S, Igarashi A, Kato T, Araki Y, Huganir RL, Dawson TM, Yanagawa T, Okamoto K, Iijima M, Sesaki H

Mitochondrial Stasis Reveals p62-Mediated Ubiquitination in Parkin-Independent Mitophagy and Mitigates Nonalcoholic Fatty Liver Disease

Cell Metab. 28: 588-604  2018 PMID:30017357 DOI:10.1016/j.cmet.2018.06.014

Liu Y, Okamoto K

The TORC1 signaling pathway regulates respiration-induced mitophagy in yeast

Biochem. Biophys. Res. Commun. 502: 76-83  2018 PMID:29787763 DOI:10.1016/j.bbrc.2018.05.123

Onishi M, Nagumo N, Iwashita S, Okamoto K

The ER membrane insertase Get1/2 is required for efficient mitophagy in yeast

Biochem. Biophys. Res. Commun. 503: 14-20  2018 PMID:29673596 DOI:10.1016/j.bbrc.2018.04.114

Xu X, Okamoto K

The Nem1-Spo7 protein phosphatase complex is required for efficient mitophagy in yeast

Biochem. Biophys. Res. Commun. 496: 51-57  2018 PMID:29305265 DOI:10.1016/j.bbrc.2017.12.163

2017

Kameoka S, Adachi Y, Okamoto K, Iijima M, Sesaki H

Phosphatidic Acid and Cardiolipin Coordinate Mitochondrial Dynamics

Trends Cell Biol. 28: 67-76  2017 PMID:28911913 DOI:10.1016/j.tcb.2017.08.011

Nagumo S, Okamoto K

Investigation of yeast mitophagy with fluorescence microscopy and Western blotting

Methods in Molecular Biology 1759: 71-83  2017 PMID:28337707 DOI:10.1007/7651_2017_11

Eiyama A, Okamoto K

Assays for mitophagy in yeast

Methods in Molecular Biology 1567:337-347.   2017 PMID:28276028 DOI:10.1007/978-1-4939-6824-4_20

Our ideal candidate (as a graduate student)

We are looking for a highly motivated person to work on our research topics as our lab member. Our lab welcomes the person who loves taking care of creatures, hand working and handcraft too. Any kind of background (such as your expertise or major) is available.

Contact

Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University,
1-3 Yamadaoka, Suita, Osaka 565-0871 Japan.

TEL: +81-6-6879-7970

E-mail: kokamoto[at]fbs.osaka-u.ac.jp (Assoc. Prof. Koji Okamoto)

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