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Elucidation of the molecular mechanism of scramblase, and the substrate specificity of flippase

Research Project

Project/Area Number 21H04770
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionOsaka University

Principal Investigator

NAGATA Shigekazu  大阪大学, 免疫学フロンティア研究センター, 特任教授(常勤) (70114428)

Co-Investigator(Kenkyū-buntansha) 瀬川 勝盛  東京医科歯科大学, 難治疾患研究所, 教授 (20542971)
櫻木 崇晴  大阪大学, 免疫学フロンティア研究センター, 特任助教(常勤) (10867906)
Project Period (FY) 2021-04-05 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥42,250,000 (Direct Cost: ¥32,500,000、Indirect Cost: ¥9,750,000)
Fiscal Year 2023: ¥12,220,000 (Direct Cost: ¥9,400,000、Indirect Cost: ¥2,820,000)
Fiscal Year 2022: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000)
Fiscal Year 2021: ¥15,340,000 (Direct Cost: ¥11,800,000、Indirect Cost: ¥3,540,000)
Keywordsフリッパーゼ / スクランブラーゼ / リン脂質 / 三次構造 / 基質特異性
Outline of Research at the Start

フォスファチジルコリン (PtdCho) は細胞膜の外層に存在する。一方、フォスファチジルセリン(PtdSer) はフリッパーゼの作用により、内層に局在する。リン脂質の非対称的な局在は様々な生物現象でスクランブラーゼの作用により崩壊する。私達は 細胞膜に存在する2個のP4-ATPases (ATP11A とATP11C) をフリッパーゼとして、TMEM16FおよびXKR8 をCa2+あるいはカスパーゼによって活性化されるスクランブラーゼとして同定した。本研究では、私達が最近決定したXKR8やATP11Cの3次構造をもとにスクランブラーゼやフリッパーゼの作用機構を解明する。

Outline of Final Research Achievements

In this study, we aimed to elucidate the physiological function of flippases (ATP11A and ATP11C) and scramblases (TMEM16F and XKR8), as well as their molecular mechanisms of action. The following results were obtained: (1) Syncytiotrophoblasts were underdeveloped in the placentas of ATP11A-deficient mice, leading to embryonic death. (2) We discovered that a point mutation in the ATP11A gene in a Japanese patient with a neurological disorder alters substrate specificity. (3) Using CryEM techniques, we determined the tertiary structure of human XKR8 and suggested the possibility of phospholipids passing through the lipid bilayer via hydrophilic amino acids inside the XKR8 molecule. (4) We observed the involvement of XK, a paralog of XKR8, in the process of exposing phosphatidylserine in inflamed tissues in response to high concentrations of ATP.

Academic Significance and Societal Importance of the Research Achievements

研究代表者はリン脂質の非対称性を維持するための酵素、それを崩壊するための分子を同定してきた。本研究ではXKR8スクランブラーゼの3次構造を明らかにし、この分子が親水性の頭部を持つリン脂質に通り道を提供していることを示した。また、フリッパーゼの点変異がリン脂質の基質特異性を変化させ、ヒトに重篤な神経疾患をもたらすこと、その遺伝子欠損は胎盤合胞体の発達不全をもたらすことを示した。これらの成果は難治性神経疾患、不妊症など理解する上でも有用であろう。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Comments on the Screening Results   Annual Research Report
  • Research Products

    (51 results)

All 2024 2023 2022 2021 Other

All Journal Article (14 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 11 results,  Open Access: 11 results) Presentation (27 results) (of which Int'l Joint Research: 8 results,  Invited: 26 results) Remarks (8 results) Patent(Industrial Property Rights) (2 results) (of which Overseas: 2 results)

  • [Journal Article] Cloning of human Type I interferon cDNAs2024

    • Author(s)
      Nagata, S.
    • Journal Title

      Proceedings of the Japan Academy, Series B

      Volume: 100 Issue: 1 Pages: 1-14

    • DOI

      10.2183/pjab.100.001

    • ISSN
      0386-2208, 1349-2896
    • Year and Date
      2024-01-11
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase2024

    • Author(s)
      Sakuragi Takaharu、Kanai Ryuta、Otani Mayumi、Kikkawa Masahide、Toyoshima Chikashi、Nagata Shigekazu
    • Journal Title

      Journal of Biological Chemistry

      Volume: 300 Issue: 3 Pages: 105755-105755

    • DOI

      10.1016/j.jbc.2024.105755

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases2023

    • Author(s)
      Sakuragi, T., Nagata, S.
    • Journal Title

      Nature Reviews Molecular Cell Biology

      Volume: 24 Issue: 8 Pages: 576-596

    • DOI

      10.1038/s41580-023-00604-z

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells2022

    • Author(s)
      Ryoden Yuta、Segawa Katsumori、Nagata Shigekazu
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 119 Issue: 7

    • DOI

      10.1073/pnas.2119286119

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inefficient development of syncytiotrophoblasts in the Atp11a-deficient mouse placenta.2022

    • Author(s)
      Ochiai Yuki、Suzuki Chigure、Segawa Katsumori、Uchiyama Yasuo、Nagata Shigekazu
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 119 Issue: 18

    • DOI

      10.1073/pnas.2200582119

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Two types of type IV P-type ATPases independently re-establish the asymmetrical distribution of phosphatidylserine in plasma membranes2022

    • Author(s)
      Miyata Yugo、Yamada Kyoko、Nagata Shigekazu、Segawa Katsumori
    • Journal Title

      Journal of Biological Chemistry

      Volume: 298 Issue: 11 Pages: 102527-102527

    • DOI

      10.1016/j.jbc.2022.102527

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The XK plasma membrane scramblase and the VPS13A cytosolic lipid transporter for ATP‐induced cell death2022

    • Author(s)
      Ryoden Yuta、Nagata Shigekazu
    • Journal Title

      BioEssays

      Volume: 44 Issue: 10 Pages: 2200106-2200106

    • DOI

      10.1002/bies.202200106

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Protocol to analyze lipid asymmetry in the plasma membrane2022

    • Author(s)
      Miyata Yugo、Segawa Katsumori
    • Journal Title

      STAR Protocols

      Volume: 3 Issue: 4 Pages: 101870-101870

    • DOI

      10.1016/j.xpro.2022.101870

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] カスパーゼによるアポトーシスの実行2022

    • Author(s)
      瀬川 勝盛, 宮田 佑吾
    • Journal Title

      医学のあゆみ

      Volume: 283(5) Pages: 329-334

    • Related Report
      2022 Annual Research Report
  • [Journal Article] リン脂質フリッパーゼとヒト遺伝性疾患2022

    • Author(s)
      瀬川 勝盛
    • Journal Title

      臨床免疫・アレルギー科

      Volume: 78(2) Pages: 238-244

    • Related Report
      2022 Annual Research Report
  • [Journal Article] クライオ電子顕微鏡でリン脂質スクランブリングのしくみに迫る2022

    • Author(s)
      櫻木 崇晴、長田 重一
    • Journal Title

      実験医学

      Volume: 40 Pages: 596-599

    • Related Report
      2021 Annual Research Report
  • [Journal Article] The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes2021

    • Author(s)
      Sakuragi Takaharu、Kanai Ryuta、Tsutsumi Akihisa、Narita Hirotaka、Onishi Eriko、Nishino Kohei、Miyazaki Takuya、Baba Takeshi、Kosako Hidetaka、Nakagawa Atsushi、Kikkawa Masahide、Toyoshima Chikashi、Nagata Shigekazu
    • Journal Title

      Nature Structural & Molecular Biology

      Volume: 28 Issue: 10 Pages: 825-834

    • DOI

      10.1038/s41594-021-00665-8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A sublethal ATP11A mutation associated with neurological deterioration causes aberrant phosphatidylcholine flipping in plasma membranes2021

    • Author(s)
      Segawa Katsumori、21人、Nagata Shigekazu
    • Journal Title

      Journal of Clinical Investigation

      Volume: 131 Issue: 18 Pages: 1-17

    • DOI

      10.1172/jci148005

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] TIM4 expression by dendritic cells mediates uptake of tumor-associated antigens and anti-tumor responses2021

    • Author(s)
      Caronni Nicoletta、19人、Nagata Shigekatzu、Benvenuti Federica
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 2237-2237

    • DOI

      10.1038/s41467-021-22535-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases2023

    • Author(s)
      長田 重一
    • Organizer
      第2回国際臨床免疫シンポジウム (鎌倉)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ブタの肝臓から50年2023

    • Author(s)
      長田 重一
    • Organizer
      第1回「AKIRA塾」(大阪)
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Regulation of phospholipid distribution by flippase and scramblase2023

    • Author(s)
      長田 重一
    • Organizer
      The 3rd Japan and Australia Meeting on Cell Death 2023(Melbourne, Australia)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 細胞膜フリッパーゼとスクランブラーゼとその異常2023

    • Author(s)
      長田 重一
    • Organizer
      実験動物中央研究所 講演会(横浜)
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 生化学に魅せられた50年ー豚の肝臓から細胞の死2023

    • Author(s)
      長田 重一
    • Organizer
      大隅基礎科学創成財団 第7期 第1回創発セミナー(On-line)
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases2023

    • Author(s)
      長田 重一
    • Organizer
      The 18th International Symposium of The Institute Network for Biomedical Sciences(Tokyo)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生化学に魅せられて2023

    • Author(s)
      長田 重一
    • Organizer
      第96回日本生化学会大会(福岡)
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 細胞膜リン脂質の非対称分布の分子機構と生理作用2023

    • Author(s)
      瀬川 勝盛
    • Organizer
      第9回JFAS研究会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞膜リン脂質の非耐用性と生理機能2023

    • Author(s)
      瀬川 勝盛
    • Organizer
      第11回日本生物工学会コロキウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞膜におけるリン脂質フリッパーゼとスクランブラーゼ(Flippase and Scramblase at the Plasma Membrane)2022

    • Author(s)
      長田 重一
    • Organizer
      第44回日本造血・免疫細胞療法学会総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞死研究から細胞膜の非対称性の研究2022

    • Author(s)
      長田 重一
    • Organizer
      金沢大学ナノ精密医学・理工学卓越大学院プログラム「Student-Selected Seminar」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞膜リン脂質の非対称性と脆弱性2022

    • Author(s)
      瀬川 勝盛
    • Organizer
      第32回日本サイトメトリー学会学術集会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞死研究から細胞膜の非対称性の研究2022

    • Author(s)
      長田 重一
    • Organizer
      初夏のセミナー(生化学若い研究者の会 近畿支部主催)
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] ATP-induced phosphatidylserine exposure and cell death2022

    • Author(s)
      長田 重一
    • Organizer
      EMBO Workshop
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] リン脂質フリッパーゼとスクランブラーゼ 作用機構とその異常による疾患2022

    • Author(s)
      長田 重一
    • Organizer
      第50回日本臨床免疫学会総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Structural analysis of the XKR8-Basigin complex that scrambles phospholipids at the plasma membrane2022

    • Author(s)
      櫻木 崇晴
    • Organizer
      The 29th Federation of Asian and Oceanian Biochemists and Molecular Biologists Conference & the 2022 Chinese Society of Biochemistry and Molecular Biology Online Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 細胞膜リン脂質スクランブラーゼXkr8-Basigin複合体の構造解析2022

    • Author(s)
      櫻木 崇晴
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Phosphatidylserine-mediated sensing and clearance of dying cells2022

    • Author(s)
      瀬川 勝盛
    • Organizer
      The 95th Annual meeting of the JBS
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ATPによるフォスファチジルセリンの暴露と細胞死2022

    • Author(s)
      長田 重一
    • Organizer
      第3回細胞死コロキウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞膜リン脂質の非対称性と生理作用2022

    • Author(s)
      瀬川 勝盛
    • Organizer
      第3回細胞死コロキウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] An XK-VPS13A complex as a lipid scramblase2022

    • Author(s)
      長田 重一
    • Organizer
      5th VPS13 Forum on the interplay of VPS13 proteins and XK in membrane lipid dynamics
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Flippase and Scramblase2021

    • Author(s)
      長田 重一
    • Organizer
      The Beutler Institute Distinguished Lecture Series at Xiamen University, Xiamen, China
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Phospholipid Flippases and Scramblases2021

    • Author(s)
      長田 重一
    • Organizer
      The 27th Annual Meeting of the Kyoto Cornea Club
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 細胞膜フリッパーゼとスクランブラーゼーその異常による病気2021

    • Author(s)
      長田 重一
    • Organizer
      第30回日本リウマチ学会近畿支部学術集会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 細胞膜リン脂質スクランブラーゼであるヒトXkr8-Basigin複合体の立体構造2021

    • Author(s)
      櫻木 崇晴
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Physiology & Pathology of plasma membrane flippases2021

    • Author(s)
      瀬川 勝盛
    • Organizer
      The 16th International Symposium of the Institute Network for Biomedical Sciences KEY FORUM 2021 International Symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Asymmetry & vulnerability of the plasma membrane2021

    • Author(s)
      瀬川 勝盛
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Remarks] 長田重一研究室

    • URL

      http://biochemi.ifrec.osaka-u.ac.jp/

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report 2021 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Research

    • URL

      https://www.ifrec.osaka-u.ac.jp/jpn/research/20230512-0800.htm

    • Related Report
      2023 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Topics

    • URL

      http://www.ifrec.osaka-u.ac.jp/jpn/topics/20221104-0830.htm

    • Related Report
      2022 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Research

    • URL

      http://www.ifrec.osaka-u.ac.jp/jpn/research/20220428-1130.htm

    • Related Report
      2022 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Research

    • URL

      http://www.ifrec.osaka-u.ac.jp/jpn/research/20220210-1000.htm

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Remarks]

    • Related Report
      2021 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Research

    • URL

      http://www.ifrec.osaka-u.ac.jp/jpn/research/20210819-0216.htm

    • Related Report
      2021 Annual Research Report
  • [Remarks] 大阪大学免疫学フロンティア研究センター News & Topics Research

    • URL

      http://www.ifrec.osaka-u.ac.jp/jpn/research/20211012-1200.htm

    • Related Report
      2021 Annual Research Report
  • [Patent(Industrial Property Rights)] XK及び/又はVPS13Aの利用2022

    • Inventor(s)
      長田重一、領田優太
    • Industrial Property Rights Holder
      長田重一、領田優太
    • Industrial Property Rights Type
      特許
    • Filing Date
      2022
    • Related Report
      2022 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] P2X7依存的細胞死調節剤2021

    • Inventor(s)
      長田重一、領田優太
    • Industrial Property Rights Holder
      長田重一、領田優太
    • Industrial Property Rights Type
      特許
    • Filing Date
      2021
    • Related Report
      2021 Annual Research Report
    • Overseas

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Published: 2021-04-28   Modified: 2025-01-30  

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