Updated on 2025/05/19

Information

 

写真a

 
YAMASHITA SHUNICHI
 
Organization
Faculty of Medical Sciences Department of Basic Medicine Assistant Professor
School of Medicine Department of Medicine(Concurrent)
Title
Assistant Professor
Contact information
メールアドレス
Tel
0926426089
Profile
細胞内小器官の動態および制御機構の解明を通して、様々な疾患と細胞内小器官の恒常性維持との関係性を明らかにする。

Degree

  • Ph.D.

Research History

  • 新潟大学大学院医歯学総合研究科・助教   

Research Interests・Research Keywords

  • Research theme: Molecular mechanisms and physiological roles of organellophagy

    Keyword: mitochondria, peroxisome, autophagy, mitophagy, pexophagy

    Research period: 2007.6

Awards

  • 新潟大学学長賞

    2017.5   新潟大学  

  • 柿内三郎記念奨励研究賞

    2011.5   日本生化学会  

Papers

  • The mitophagy receptors BNIP3 and NIX mediate tight attachment and expansion of the isolation membrane to mitochondria.

    Yamashita SI, Arai R, Hada H, Padman BS, Lazarou M, Chan DC, Kanki T, Waguri S

    The Journal of cell biology   224 ( 7 )   2025.7   ISSN:0021-9525

     More details

    Language:English  

    ミトコンドリアオートファジーの分子機構を解明し、その微細構造の取得に成功した。

    DOI: 10.1083/jcb.202408166

    PubMed

  • Atg44/Mdi1/mitofissin facilitates Dnm1-mediated mitochondrial fission

    Furukawa, K; Hayatsu, M; Okuyama, K; Fukuda, T; Yamashita, SI; Inoue, K; Shibata, S; Kanki, T

    AUTOPHAGY   20 ( 10 )   2314 - 2322   2024.10   ISSN:1554-8627 eISSN:1554-8635

     More details

    Language:English   Publisher:Autophagy  

    Mitochondria undergo fission and fusion, and their coordinated balance is crucial for maintaining mitochondrial homeostasis. In yeast, the dynamin-related protein Dnm1 is a mitochondrial fission factor acting from outside the mitochondria. We recently reported the mitochondrial intermembrane space protein Atg44/mitofissin/Mdi1/Mco8 as a novel fission factor, but the relationship between Atg44 and Dnm1 remains elusive. Here, we show that Atg44 is required to complete Dnm1-mediated mitochondrial fission under homeostatic conditions. Atg44-deficient cells often exhibit enlarged mitochondria with accumulated Dnm1 and rosary-like mitochondria with Dnm1 foci at constriction sites. These mitochondrial constriction sites retain the continuity of both the outer and inner membranes within an extremely confined space, indicating that Dnm1 is unable to complete mitochondrial fission without Atg44. Moreover, accumulated Atg44 proteins are observed at mitochondrial constriction sites. These findings suggest that Atg44 and Dnm1 cooperatively execute mitochondrial fission from inside and outside the mitochondria, respectively. Abbreviation: ATG: autophagy related; CLEM: correlative light and electron microscopy; EM: electron microscopy; ER: endoplasmic reticulum; ERMES: endoplasmic reticulum-mitochondria encounter structure; GA: glutaraldehyde; GFP: green fluorescent protein; GTP: guanosine triphosphate: IMM: inner mitochondrial membrane; IMS: intermembrane space; OMM: outer mitochondrial membrane; PB: phosphate buffer; PBS: phosphate-buffered saline; PFA: paraformaldehyde; RFP: red fluorescent protein; WT: wild type.

    DOI: 10.1080/15548627.2024.2360345

    Web of Science

    Scopus

    PubMed

  • Comprehensive analysis of non-selective and selective autophagy in yeast atg mutants and characterization of autophagic activity in the absence of the Atg8 conjugation system

    Ginevskaia, T; Innokentev, A; Furukawa, K; Fukuda, T; Hayatsu, M; Yamashita, S; Inoue, K; Shibata, S; Kanki, T

    JOURNAL OF BIOCHEMISTRY   176 ( 3 )   217 - 227   2024.6   ISSN:0021-924X eISSN:1756-2651

     More details

    Language:English   Publisher:Journal of Biochemistry  

    Most autophagy-related genes, or ATG genes, have been identified through studies using budding yeast. Although the functions of the ATG genes are well understood, the contributions of individual genes to non-selective and various types of selective autophagy remain to be fully elucidated. In this study, we quantified the activity of non-selective autophagy, the cytoplasm-to-vacuole targeting (Cvt) pathway, mitophagy, endoplasmic reticulum (ER)-phagy and pexophagy in all Saccharomyces cerevisiae atg mutants. Among the mutants of the core autophagy genes considered essential for autophagy, the atg13 mutant and mutants of the genes involved in the two ubiquitin-like conjugation systems retained residual autophagic functionality. In particular, mutants of the Atg8 ubiquitin-like conjugation system (the Atg8 system) exhibited substantial levels of non-selective autophagy, the Cvt pathway and pexophagy, although mitophagy and ER-phagy were undetectable. Atg8-system mutants also displayed intravacuolar vesicles resembling autophagic bodies, albeit at significantly reduced size and frequency. Thus, our data suggest that membranous sequestration and vacuolar delivery of autophagic cargo can occur in the absence of the Atg8 system. Alongside these findings, the comprehensive analysis conducted here provides valuable datasets for future autophagy research.

    DOI: 10.1093/jb/mvae042

    Web of Science

    Scopus

    PubMed

  • Mitophagy mediated by BNIP3 and NIX protects against ferroptosis by downregulating mitochondrial reactive oxygen species Reviewed International journal

    @Yamashita SI, @Sugiura Y, @Matsuura Y, @Maeda R, @Inoue K, @Furukawa K, @Fukuda T, @Chan DC, @Kanki T

    Cell Death and Differentiation   2024.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Mitophagy plays an important role in the maintenance of mitochondrial homeostasis and can be categorized into two types: ubiquitin-mediated and receptor-mediated pathways. During receptor-mediated mitophagy, mitophagy receptors facilitate mitophagy by tethering the isolation membrane to mitochondria. Although at least five outer mitochondrial membrane proteins have been identified as mitophagy receptors, their individual contribution and interrelationship remain unclear. Here, we show that HeLa cells lacking BNIP3 and NIX, two of the five receptors, exhibit a complete loss of mitophagy in various conditions. Conversely, cells deficient in the other three receptors show normal mitophagy. Using BNIP3/NIX double knockout (DKO) cells as a model, we reveal that mitophagy deficiency elevates mitochondrial reactive oxygen species (mtROS), which leads to activation of the Nrf2 antioxidant pathway. Notably, BNIP3/NIX DKO cells are highly sensitive to ferroptosis when Nrf2-driven antioxidant enzymes are compromised. Moreover, the sensitivity of BNIP3/NIX DKO cells is fully rescued upon the introduction of wild-type BNIP3 and NIX, but not the mutant forms incapable of facilitating mitophagy. Consequently, our results demonstrate that BNIP3 and NIX-mediated mitophagy plays a role in regulating mtROS levels and protects cells from ferroptosis.

    DOI: 10.1038/s41418-024-01280-y

  • Imeglimin mitigates the accumulation of dysfunctional mitochondria to restore insulin secretion and suppress apoptosis of pancreatic β-cells from db/db mice. Reviewed International journal

    @Aoyagi K, @Nishikawa C, @Nakamichi Y, @Yamashita SI, @Kanki T, @Ohara-Imaizumi M.

    Scientific Reports   2024.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41598-024-56769-w

  • Mitophagy Responds to the Environmental Temperature and Regulates Mitochondrial Mass in Adipose Tissues

    Yamashita S.I., Kanki T.

    Advances in experimental medicine and biology   1461   229 - 243   2024   ISSN:00652598 ISBN:978-981-97-4586-9 eISSN:2214-8019

     More details

    Language:English   Publisher:Advances in experimental medicine and biology  

    There are at least two types of adipose tissues in the body, defined as brown adipose tissues (BATs) and white adipose tissues (WATs). These tissues comprise brown and white adipocytes, respectively. The adipocytes are commonly endowed with mitochondria, but they have diverse characteristics and roles. Brown adipocytes have abundant mitochondria that contribute to the β-oxidation of fatty acids to produce chemical energy and the production of heat via uncoupling of the mitochondrial membrane potential from ATP synthesis. Alternatively, white adipocytes have fewer mitochondria that contribute to the generation of free fatty acids via lipogenesis by providing key intermediates. Besides the described types of adipocytes, brown-like adipocytes, termed beige adipocytes, are developed in WAT depots during cold exposure. Beige adipocytes also contribute to thermogenesis. Notably, beige adipocytes may transform into white-like adipocytes after the withdrawal of cold exposure. This process is marked by the elimination of mitochondria through the activation of mitochondria autophagy (mitophagy). This review aims to describe the mitophagy that occurs during the beige-to-white transition and discuss recent insights into the molecular mechanisms of this transformation. Additionally, we describe the mitophagy monitoring strategy in adipose tissues using three independent reporter systems and discuss the availabilities and limitations of the method.

    DOI: 10.1007/978-981-97-4584-5_16

    Web of Science

    Scopus

    PubMed

  • Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein. Reviewed International journal

    @Fukuda T, @Saigusa T, @Furukawa K, @Inoue K, @Yamashita SI, @Kanki T.

    Autophagy   2023.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/15548627.2023.2214029

  • The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy Reviewed International journal

    @Fukuda T, @Furukawa K, @Maruyama T, @Yamashita SI, @Noshiro D, @Song C, @Ogasawara Y, @Okuyama K, @Alam JM, @Hayatsu, M, @Saigusa T, @Inoue K, @Ikeda K, @Takai A, @Chen L, @Lahiri V, @Okada Y, @Shibata S, @Murata K, @Klionsky DJ, @Noda NN, @Kanki T.

    Molecular Cell   2023.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.molcel.2023.04.022

  • TIM23 facilitates PINK1 activation by safeguarding against OMA1-mediated degradation in damaged mitochondria. Reviewed International journal

    @Akabane S, @Watanabe K, @Kosako H, @Yamashita SI, @Nishino K, @Kato M, @Sekine S, @Kanki T, @Matsuda N, @Endo T, @Oka T.

    Cell Reports   2023.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.celrep.2023.112454

  • Myeloid-associated differentiation marker is an essential host factor for human parechovirus PeV-A3 entry Reviewed International journal

    @Watanabe K, @Oka T, @Takagi H, @Anisimov S, @Yamashita SI, @Katsuragi Y, @Takahashi M, @Higuchi M, @Kanki T, @Saitoh A, @Fujii M

    Nature Communications   2023.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41467-023-37399-8

  • A new beta cell-specific mitophagy reporter mouse shows that metabolic stress leads to accumulation of dysfunctional mitochondria despite increased mitophagy Reviewed International journal

    @Aoyagi K, @Yamashita SI, @Akimoto Y, @Nishikawa C, @Nakamichi Y, @Udagawa H, @Abe M, @Sakimura K, @Kanki T, @Ohara-Imaizumi M

    Diabetologia   2023.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/s00125-022-05800-8

  • Mitophagy reporter mouse analysis reveals increased mitophagy activity in disuse-induced muscle atrophy Reviewed International journal

    @Yamashita SI, @Kyuuma M, @Inoue K, @Hata Y, @Kawada R, @Yamabi M, @Fujii Y, @Sakagami J, @Fukuda T, @Furukawa K, @Tsukamoto S, @Kanki T

    Journal of Cellular Physiology   2021.11

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/jcp.30404

  • Fis1 ablation in the male germline disrupts mitochondrial morphology and mitophagy, and arrests spermatid maturation Reviewed International journal

    @Varuzhanyan G, @Ladinsky MS, @Yamashita SI, @Abe M, @Sakimura K, @Kanki T, @Chan DC

    Development   2021.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1242/dev.199686

  • The optineurin/TIA1 pathway inhibits aberrant stress granule formation and reduces ubiquitinated TDP-43 Reviewed International journal

    @Kakihana T, @Takahashi M, @Katsuragi Y, @Yamashita SI, @Sango J, @Kanki T, @Onodera O, @Fujii M

    iScience   2021.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.isci.2021.102733

  • MITOL promotes cell survival by degrading Parkin during mitophagy Reviewed International journal

    @Shiiba I, @Takeda K, @Nagashima S, @Ito N, @Tokuyama T, @Yamashita SI, @Kanki T, @Komatsu T, @Urano Y, @Fujikawa Y, @Inatome R, @Yanagi S

    EMBO Reports   2021.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.15252/embr.201949097

  • Association and dissociation between the mitochondrial Far complex and Atg32 regulate mitophagy Reviewed International journal

    @Innokentev A, @Furukawa K, @Fukuda T, @Saigusa T, @Inoue K, @Yamashita SI, @Kanki T

    Elife   2020.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.7554/eLife.63694

  • Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast Reviewed International journal

    @Fukuda T, @Ebi Y, @Saigusa T, @Furukawa K, @Yamashita SI, @Inoue K, @Kobayashi D, @Yoshida Y, @Kanki T

    Elife   2020.11

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.7554/eLife.61245

  • FKBP8 LIRL-dependent mitochondrial fragmentation facilitates mitophagy under stress conditions Reviewed International journal

    @Yoo SM, @Yamashita SI, @Kim H, @Na D, @Lee H, @Kim SJ, @Cho DH, @Kanki T, @Jung YK

    FASEB Journal   2020.2

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1096/fj.201901735R

  • Gemcitabine induces Parkin-independent mitophagy through mitochondrial-resident E3 ligase MUL1-mediated stabilization of PINK1 Reviewed International journal

    @Igarashi R, @Yamashita SI, @Yamashita T, @Inoue K, @Fukuda T, @Fukuchi T, @Kanki T

    Scientific Reports   2020.1

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41598-020-58315-w

  • Glaucoma-Associated Mutations in the Optineurin Gene Have Limited Impact on Parkin-Dependent Mitophagy Reviewed International journal

    @Chernyshova K, @Inoue K, @Yamashita SI, @Fukuchi T, @Kanki T

    Investigative Ophthalmology and Visual Science   2019.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1167/iovs.19-27184

  • The PP2A-like Protein Phosphatase Ppg1 and the Far Complex Cooperatively Counteract CK2-Mediated Phosphorylation of Atg32 to Inhibit Mitophagy Reviewed International journal

    @Furukawa K, @Fukuda T, @Yamashita SI, @Saigusa T, @Kurihara Y, @Yoshida Y, @Kirisako H, @Nakatogawa H, @Kanki T

    Cell Reports   2018.6

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.celrep.2018.05.064

  • Detection of Hypoxia-Induced and Iron Depletion-Induced Mitophagy in Mammalian Cells Reviewed International journal

    @Yamashita SI, @Kanki T

    Methods in Molecular Biology, Mitophagy   2018.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/7651_2017_19

  • Detection of Iron Depletion- and Hypoxia-induced Mitophagy in Mammalian Cells Reviewed International journal

    @Yamashita SI, @Kanki T

    Methods in Molecular Biology, Mitochondrial Bioenergetics   2018.5

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/978-1-4939-7831-1_18

▼display all

Books

  • 温度ストレスによる生体ダイナミクス

    @山下俊一(Role:Sole author)

    エヌ・ティー・エス  2023.5 

     More details

    Language:Japanese   Book type:Scholarly book

Presentations

MISC

Professional Memberships

  • 日本生化学会

  • 日本ミトコンドリア学会

  • 日本細胞生物学会

  • 日本分子生物学会

Academic Activities

  • Screening of academic papers

    Role(s): Peer review

    2023

     More details

    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:5

  • Screening of academic papers

    Role(s): Peer review

    2022

     More details

    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:8

Research Projects

  • 2型糖尿病関連SNPとミトコンドリア機能低下との関係性解明による新規疾患発症機序の提唱

    2023 - 2024

    鈴木謙三記念医科学応用研究財団・調査研究助成金

      More details

    Authorship:Principal investigator  Grant type:Contract research

  • レセプター依存的マイトファジーの誘導制御と生理機能の解明

    Grant number:23K23878  2022.4 - 2025.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    神吉 智丈, 井上 敬一, 山下 俊一, 福田 智行

      More details

    Grant type:Scientific research funding

    ミトコンドリアは、細胞が必要とするエネルギーを作る非常に重要な場所である。従来の研究は、ミトコンドリアがどのようにして作られてくるかに着目していたが、本研究は、機能が悪くなったミトコンドリアを取り除く(分解する)現象であるマイトファジーに着目し、その生理機能を明らかにしようとするものである。具体的には、マイトファジーの誘導が抑制された培養細胞やマウスを用いて、どのような異常が生じるのかを観察する。

    CiNii Research

  • 抗がん剤耐性に関与する新奇マイトファジーの分子機構解明と化学療法への応用

    2022 - 2024

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

      More details

    Grant type:Scientific research funding

  • 哺乳類ペルオキシソーム分解の分子機構とその生理的意義に関する研究

    2010 - 2012

    Japan Society for the Promotion of Science  Research Fellowships for Young Scientists

      More details

    Authorship:Principal investigator  Grant type:Joint research

Class subject

  • 生理学実習

    2025.9 - 2025.10  

  • 人体構造と機能III

    2025.5  

  • 生理学

    2025.4 - 2026.3  

  • 生理学実習

    2024.9 - 2024.10  

  • 生理学

    2024.4 - 2025.3  

  • 人体構造と機能III

    2024.4 - 2024.9   First semester

▼display all

Visiting, concurrent, or part-time lecturers at other universities, institutions, etc.

  • 2024  新潟大学大学院医歯学総合研究科  Classification:Affiliate faculty  Domestic/International Classification:Japan