Molecular basis of new protein quality control systems depending on the pH gradient between the ER and the Golgi

• Project/Area Number: 15H04335
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tohoku University
• Principal Investigator: Inaba Kenji 東北大学, 多元物質科学研究所, 教授 (10423039)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000); Fiscal Year 2017: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2016: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
• Keywords: タンパク質品質管理 / 小胞体 / ゴルジ体 / Ｘ線結晶構造解析 / ERp44 / PDIファミリー / pH / 亜鉛 / 蛋白質 / 酵素 / PDI / 細胞 / X線結晶構造解析 / レドックス

Outline of Final Research Achievements

ERp44 is a PDI-family member protein that transports back ER-resident enzymes and immature secretory proteins from the Golgi to the ER and thereby conducts protein quality control in the early secretory pathway. In this reserach project, we succeeded in crystal structure analysis of ERp44 at pH7.5 and pH6.5. Based on the structural information, we performed a series of biochemical, biophysical and cell biological studies. Consequently, we revealed the molecular mechanism by which ERp44 regulates the substrate binding and release in a pH-dependent manner (Watanabe et al., PNAS 2017).

Research Products

• [Int'l Joint Research] San Raffaele Scientific Institute(イタリア)
• [Int'l Joint Research] San Raffaele Scientific Institute(Italy)
• [Journal Article] The Highly Dynamic Nature of ERdj5 Is Key to Efficient Elimination of Aberrant Protein Oligomers through ER-Associated Degradation. (2017)
  • Author(s): Maegawa KI, Watanabe S#, Noi K#, Okumura M#, Amagai Y#, Inoue M, Ushioda R, Nagata K, Ogura T, Inaba K.(#equal contribution)
  • Journal Title: Structure Volume: 25 Issue: 6 Pages: 846-857
  • DOI: 10.1016/j.str.2017.04.001
  • Peer Reviewed / Open Access
• [Journal Article] Preparation of Selenoinsulin as a Long-Lasting Insulin Analogue (2017)
  • Author(s): Kenta Arai+, Toshiki Takei+, Masaki Okumura+, Satoshi Watanabe+, Yuta Amagai, Yuya Asahina, Luis Moroder, Hironobu Hojo, Kenji Inaba, and Michio Iwaoka
  • Journal Title: Angew. Chem. Int. Ed. Volume: 印刷中 Issue: 20 Pages: 5522-5526
  • DOI: 10.1002/anie.201701654
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER-Golgi interface. (2017)
  • Author(s): Watanabe, S., Harayama, M., Kanemura, S., Sitia, R. and Inaba, K.
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: in press Issue: 16 Pages: 3224-3232
  • DOI: 10.1073/pnas.1621426114
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Cysteinyl-tRNA synthetase governs cysteine polysulfidation and mitochondrial bioenergetics (2017)
  • Author(s): Akaike Takaaki、、、Nishida Motohiro（4）、、、、、、Fujii Shigemoto（20）、、、Motohashi Hozumi（26）
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 1177-1177
  • DOI: 10.1038/s41467-017-01311-y
  • NAID: 120007134656
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Preparation of selenoinsulin as a long-lasting insulin analog (2017)
  • Author(s): Arai, K.#, Takei, T.#, Okumura, M.#, Watanabe, S.#, Amagai, Y., Hojo, H.*, Inaba, K.* and Iwaoka, M.*
  • Journal Title: Angewandte Chemie Volume: in press
  • Peer Reviewed
• [Journal Article] The highly dynamic nature of ERdj5 is key to efficient elimination of aberrant protein oligomers through ER-associated degradation (2017)
  • Author(s): Maegawa, K., Watanabe, S., Noi, K., Okumura, M., Amagai, Y., Inoue, M., Ushioda, R., Nagata, K., Ogura, T. and Inaba, K
  • Journal Title: Structure Volume: in press
  • Peer Reviewed
• [Journal Article] Redox-assisted regulation of Ca2+ homeostasis in the endoplasmic reticulum by ERdj5 (2016)
  • Author(s): Ushioda, R., Miyamoto, A., Inoue, M., Watanabe, S., Okumura, M., Maegawa, K., Uegaki, K., Fujii, S., Fukuda, Y., Umitsu, M., Takagi, J., Inaba, K., Mikoshiba, K., Nagata, K.
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 113 Pages: 6055-6063
  • Peer Reviewed
• [Journal Article] Human ER Oxidereductin-1a (Ero1a) undergoes dual regulation through complementary redox interactions with Protein Disulfide Isomerase. (2016)
  • Author(s): Kanemura, S., Okumura, M., Yutani, K., Ramming, T., Hikima, T., Appenzeller-Herzog, C., Akiyama, S., and Inaba, K.
  • Journal Title: J. Biol. Chem. Volume: 291 Pages: 23952-23964
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The membrane topology of Vitamin K Epoxide Reductase is conserved between human isoforms and the bacterial enzyme (2016)
  • Author(s): Cao, Z, van Lith, M., Mitchell, L. J., Pringle, M. A., Inaba, K. and Bulleid, N. J.
  • Journal Title: Biochem. J Volume: 473 Issue: 7 Pages: 851-858
  • DOI: 10.1042/bj20151223
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Cysteines 208 and 241 in Ero1 are required for maximal catalytic turnover (2015)
  • Author(s): T. Ramming, S. Kanemura, M. Okumura, K. Inaba and C. Appenzeller-Herzog.
  • Journal Title: Redox Biology Volume: 7 Pages: 14-20
  • DOI: 10.1016/j.redox.2015.11.004
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] One-dimensional sliding of p53 along DNA is accelerated in the presence of Ca(2+) or Mg(2+) at millimolar concentrations (2015)
  • Author(s): Murata A, Ito Y, Kashima R, Kanbayashi S, Nanatani K, Igarashi C, Okumura M, Inaba K, Tokino T, Takahashi S, Kamagata K
  • Journal Title: JOURNAL OF MOLECULAR BIOLOGY Volume: 427 Issue: 16 Pages: 2663-2678
  • DOI: 10.1016/j.jmb.2015.06.016
  • Peer Reviewed / Open Access
• [Journal Article] Structural basis of a Ni acquisition cycle for [NiFe]-hydrogenase by HypA and its enhancer. (2015)
  • Author(s): Watanabe, S., Kawashima, T., Nishitani, Y., Kanai, T., Wada, T., Inaba, K., Atomi, H., Imanaka, T. and Miki, K.
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 112 Issue: 25 Pages: 7701-7706
  • DOI: 10.1073/pnas.1503102112
  • Peer Reviewed / Open Access
• [Journal Article] A PDI-catalyzed thiol/disulfide switch regulates the production of hydrogen peroxide by human Ero1 (2015)
  • Author(s): T. Ramming, M. Okumura, S. Kanemura, S. Baday, J. Birk, S. Moes, P. Jenö, S. Bernèche, K. Inaba and C. Appenzeller-Herzog.
  • Journal Title: Free Radic Biol Med. Volume: 83 Pages: 361-372
  • DOI: 10.1016/j.freeradbiomed.2015.02.011
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Structures and functions of protein disulfide isomerase family members involved in proteostasis in the endoplasmic reticulum. (2015)
  • Author(s): Okumura M, Kadokura H, Inaba K.
  • Journal Title: Free Radic Biol Med. Volume: 83 Pages: 314-322
  • DOI: 10.1016/j.freeradbiomed.2015.02.010
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] 新規PDIファミリータンパク質ERp46の構造と機能 (2015)
  • Author(s): 奥村 正樹、金村 進吾、稲葉 謙次
  • Journal Title: 日本生物物理学会会報誌 Volume: 55 Pages: 34-36
  • NAID: 130004794735
  • Peer Reviewed
• [Presentation] The highly dynamic nature of ERdj5 plays a key role in efficient ER-associated degradation (2018)
  • Author(s): Inaba, K.
  • Organizer: CLS Tokyo Tech. International Forum 2018
  • Int'l Joint Research / Invited
• [Presentation] Structural and Mechanistic basis of pH- and Zn2+-dependent regulation of ERp44 for protein quality control in the early secretory pathway (2017)
  • Author(s): Inaba, K.
  • Organizer: ER & Redox club meeting
  • Int'l Joint Research
• [Presentation] How do PDI family member proteins act on nascent chains to catalyze their oxidative protein (2017)
  • Author(s): 奥村 正樹、平山 千尋、野井 健太郎、町田 幸大、今高 寛晃、小椋 光、稲葉 謙次
  • Organizer: 第17回日本蛋白質科学会年会
  • Invited
• [Presentation] Structural basis of redox-dependent regulation of Sarco/Endoplasmic reticulum Ca2+-ATPase 2b (SERCA2b) (2017)
  • Author(s): 稲葉謙次
  • Organizer: 日本生物物理学会年会
  • Invited
• [Presentation] システインの酸化還元を介した新たなタンパク質品質管理機構の構造基盤 (2017)
  • Author(s): 稲葉謙次
  • Organizer: 大阪大学蛋白質研究所セミナー
  • Invited
• [Presentation] Zn-dependent regulation of the protein quality control by ERp44 in the early secretory pathway (2016)
  • Author(s): Harayama, M., Watanabe, S., Amagai, Y., Sannino, S., Sitia, R., Inaba, K.
  • Organizer: 第39回日本分子生物学会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2016-11-30
• [Presentation] 小胞体タンパク質品質管理に関与するERp44のpHと亜鉛イオンによる機能制御 (2016)
  • Author(s): 渡部 聡, 原山麻奈美, 天貝佑太, 増井翔史, Sara Sannino, Roberto Sitia, 稲葉謙次
  • Organizer: 第８９回日本生化学会大会
  • Place of Presentation: 仙台国際センター（宮城県仙台市）
  • Year and Date: 2016-09-25
• [Presentation] How do PDI family member proteins act on unfolded/misfolded proteins to ensure protein quality control in the ER. (2016)
  • Author(s): Inaba, K.
  • Organizer: Nascent chain biology meeting 2016
  • Place of Presentation: 富士レークホテル（山梨県河口湖町）
  • Year and Date: 2016-09-01
  • Int'l Joint Research / Invited
• [Presentation] Structural basis of pH- and zinc-dependent protein quality control by ERp44 (2016)
  • Author(s): Watanabe, S., Harayama, M., Amagai, Y., Sannino, S., Masui, S., Sitia, R. and Inaba, K.
  • Organizer: Nascent chain biology meeting 2016
  • Place of Presentation: 富士レークホテル（山梨県河口湖町）
  • Year and Date: 2016-09-01
  • Int'l Joint Research
• [Presentation] 亜鉛イオンによるERp44を介した小胞体タンパク質品質管理機構の分子基盤 (2016)
  • Author(s): 渡部 聡, 原山麻奈美, 天貝佑太, 増井翔史, Sara Sannino, Roberto Sitia, 稲葉謙次
  • Organizer: 第１６回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場（福岡県福岡市）
  • Year and Date: 2016-06-07
• [Presentation] Dynamic natures of PDI family members in catalysis of oxidative protein folding and ER associated degradation (2015)
  • Author(s): Inaba, K
  • Organizer: Symposium: From cytosol to ER; Translation, translocation and modification
  • Place of Presentation: 東北大学片平キャンパス生命科学研究科プロジェクト棟（仙台市）
  • Year and Date: 2015-11-30
  • Int'l Joint Research / Invited
• [Presentation] Dynamic natures of PDI family member proteins that act on nascent chains in the endoplasmic reticulum (2015)
  • Author(s): Inaba, K
  • Organizer: Nascent chain biology meeting
  • Place of Presentation: 東京大学本郷キャンパス一条ホール（東京）
  • Year and Date: 2015-10-01
  • Int'l Joint Research / Invited
• [Presentation] Real-time monitoring of PDI-catalyzed oxidative protein folding by high-speed atomic force microscopy (2015)
  • Author(s): 奥村正樹、野井健太郎，金村進吾、増井翔史、引間孝明、秋山修志、小椋光、稲葉謙次
  • Organizer: 第53回 生物物理学会年会
  • Place of Presentation: 金沢大学角間キャンパス自然科学本館（金沢市）
  • Year and Date: 2015-09-13
  • Invited
• [Presentation] Dynamic natures of PDI family members in catalysis of oxidative protein folding and ER associated degradation (2015)
  • Author(s): Inaba, K
  • Organizer: EMBO meeting
  • Place of Presentation: Birmingham, UK
  • Year and Date: 2015-09-05
  • Int'l Joint Research / Invited
• [Presentation] Dynamic natures of PDI family members in catalysis of oxidative protein folding and ER associated degradation (2015)
  • Author(s): Inaba, K
  • Organizer: Case Western Reserve University-Tohoku University joint symposium
  • Place of Presentation: Cleaveland, USA
  • Year and Date: 2015-07-29
  • Int'l Joint Research / Invited
• [Presentation] Dual conformations of ERdj5 play a significant role in acceleration of the ER associated degradation. (2015)
  • Author(s): Inaba, K
  • Organizer: ER & Redox club meeting
  • Place of Presentation: Venice, Italy
  • Year and Date: 2015-04-15
  • Int'l Joint Research
• [Book] Oxidative folding of Peptides and Proteins (2018)
  • Author(s): M. Okumura, S. Watanabe, and K. Inaba
  • Publisher: Royal Society of Chemistry
• [Book] 分子研レターズ (2017)
  • Author(s): 金村 進吾、奥村 正樹、稲葉 謙次
  • Publisher: 分子研
• [Remarks] 東北大学多元物質科学研究所生体分子構造研究分野 稲葉研究室
  • URL: http://www.tagen.tohoku.ac.jp/labo/inaba/
• [Remarks] 東北大学 多元物質科学研究所 生体分子構造研究分野 稲葉研究室
  • URL: http://www.tagen.tohoku.ac.jp/labo/inaba/
• [Remarks] 細胞内pH変化を利用したタンパク質品質管理のメカニズム ‐pHセンシング機構の構造基盤を解明‐
  • URL: http://www2.tagen.tohoku.ac.jp/lab/news_press/20170404/
• [Remarks] 東北大学生命科学研究科分子生命科学専攻 稲葉謙次
  • URL: http://www.lifesci.tohoku.ac.jp/teacher/t_inaba/
• [Remarks] 東北大学多元物質科学研究所 生体分子構造研究分野ホームページ
  • URL: http://www.tagen.tohoku.ac.jp/labo/inaba/