Tokyo Metropolitan Institute of Medical Science: Laboratory of Protein Metabolism

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Original Articles

2021

  1. Kaiho-Soma A, Akizuki Y, Igarachi K, Endo A, Shoda T, Kawase Y, Demizu Y, Naito M, Saeki Y, Tanaka K, *Ohtake F. (2021) TRIP12 promotes small molecule-induced degradation of BRD4 through K29/K48 branched ubiquitin chains. Mol Cell 81, 1411-1424.e7. (Publisher link, Previews)
  2. Nakabayashi O, Takahashi H, Moriwaki K, Komazawa-Sakon S, Ohtake-F, Murai Y, Koyahara Y, Saeki Y, Yoshida Y, Yamazaki S, Tokunaga F, Sawasaki T, *Nakano H. (2021) MIND bomb 2 prevents RIPK1 kinase activity-dependent and -independent apoptosis through ubiquitylation of cFLIPL. Commun Biol. 4,80. (Publisher link)
  3. Imada T, Shimi T, Kaiho A, Saeki Y, *Kimura H. (2021) RNA polymerase II condensate formation and association with Cajal and histone locus bodies in living human cells. Genes Cell AOP (Publisher link)

2020

  1. Yasuda S, Tsuchiya H (co-1st), Kaiho A (co-1st), Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernandez-Busnadiego R, *Tanaka K, *Saeki Y. (2020) Stress- and ubiquitylation-dependent phase separation of the proteasome. Nature 578, 296-300. (Publisher link, EurekAlert!, Faculty Opinions, highlight in Cell Res!)
  2. Fuseya Y, Fujita H, Kim M, Ohtake F, Nishide A, Sasaki K, Saeki Y, Tanaka K, Takahashi R, *Iwai K. (2020) The HOIL-1L ligase modulates immune signalling and cell death via monoubiquitination of LUBAC. Nat Cell Biol. 22, 663-673.
  3. Matsuo Y, Tesina P, Nakajima S, Mizuno M, Endo A, Buschauer R, Cheng J, Shounai O, Ikeuchi K, Iwasaki S, Saeki Y, Becker T, Beckmann R, Inada T. (2020) RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nat Stuct Mol Biol. 27,323-332.
  4. *Nishiyama A, Mulholland C, Bultmann S, Kori A, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, *Arita K, *Leonhardt H,  *Nakanishi M. (2020) Two distinct modes of DNMT1 recruitment ensure the stable maintenance DNA methylation. Nat Commun. 11, 1222.
  5. Oikawa D, Sato Y, Ohtake F, Komakura K, Hanada K, Sugawara K, Terawaki S, Mizukami Y, Phuong HT, Iio K, Obika S, Fukushi M, Irie T, Tsuruta D, Sakamoto S, Tanaka K, Saeki Y, Fukai S, *Tokunaga F. (2020) Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses. Commun Biol. 3, 163.

2019

  1. Sato Y, Tsuchiya H (co-1st), Yamagata A, Okatsu K, Tanaka, K, *Saeki Y, *Fukai S. (2019) Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Nat Commun. 10, 5708. (Publisher link, Commentary)
  2. Ikeuchi K, Tesina P, Matsuo Y, Sugiyama T, Cheng J, Saeki Y, Tanaka T, Becker T, *Beckmann R, *Inada, T. (2019) Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J. e100276.
  3. *Masuda Y, Saeki Y, Arai N, Kawai H, Kukimoto I, Tanaka K, Masutani C. (2019) Stepwise multipolyubiquitantion of p53 by the E6AP-E6 ubiquitin ligase complex. J Biol Chem. 294, 14860-14875.

2018

  1. Tsuchiya H, Burana D, Ohtake F, Arai N, Kaiho A, Komada M, *Tanaka K, *Saeki Y. (2018) Ub-ProT reveals global length and composition of protein ubiquitylation in cells. Nat Commun. 9, 524. (Publisher link, Commentary)
  2. *Ohtake F, Tsuchiya H, Saeki Y, *Tanaka K. (2018) K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains. Proc Natl Acad Sci USA. 115, E1401-E1408. (Publisher link)
  3. Xie X, Matsumoto S, Endo A, Fukushima T, Kawahara H, Saeki Y, *Komada M. (2018) Deubiquitylases USP5 and USP13 are recruited to and regulate heat-induced stress granules through their deubiquitylating activities. J Cell Sci. 131, jcs210856.
  4. Wu W, Rokutanda N, Takeuchi J, Lai Y, Maruyama R, Togashi Y, Nishikawa H, Arai N, Miyoshi Y, Suzuki N, Saeki Y, Tanaka K, *Ohta T. (2018) HERC2 facilitates BLM and WRN helicase complex interaction with RPA to suppress G-quadruplex DNA. Cancer Res. 78, 6371-6385
  5. Tomita T, Hirayama S, Sakurai Y, Ohte Y, Yoshihara H, Saeki Y, Hamazaki J, *Murata S. (2018) Specific modification of aged proteasomes revealed by tag-exchangeable knock-in mice. Mol Cell Biol. 39, e00426-18

2017 (selected papers)

  1. Tsuchiya H, Ohtake F, Arai N, Kaiho A, Yasuda S, *Tanaka K, *Saeki Y. (2017) In vivo ubiquitin linkage-type analysis reveals that the Cdc48-Rad23/Dsk2 axis contributes to K48-linked chain specificity of the proteasome. Mol Cell 66, 488-502. (Publisher link, Commentary)
  2. Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K, Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, *Suetake I, *Arita K, *Nakanishi M. (2017) Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance. Mol Cell 68, 350-360.
  3. Sato Y, Okatsu K, Saeki Y, Yamano K, Matsuda N, Kaiho A, Yamagata A, Goto-Ito S, Ishikawa M, Hashimoto Y, Tanaka K, *Fukai S. (2017) Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30. Nat Struct Mol Biol. 24, 911-919.
  4. *Yoshida Y, Yasuda S, Fujita T, Hamasaki M, Murakami A, Kawawaki J, Iwai K, Saeki Y, Yoshimori T, Matsuda M, *Tanaka K. (2017) Ubiquitination of exposed glycoproteins by SCFFBXO27 directs damaged lysosomes for autophagy. Proc Natl Acad Sci. USA. 114, 8574-8579.
  5. Matsuo Y, Ikeuchi K, Saeki Y, Iwasaki S, Schmidt C, Udagawa T, Sato F, Tsuchiya T, Becker T, Tanaka K, Ingolia NT, Beckmann R, *Inada T. (2017) Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat Commun. 8, 159.
  6. Uddin MM, Ohigashi I, Motosugi R, Nakayama T, Sakata M, Hamazaki J, Nishito Y, Rode I, Tanaka K, Takemoto T, Murata S, *Takahama Y. (2017) Foxn1-β5t transcriptional axis controls CD8+ T cell production in the thymus. Nat Commun. 8, 14419

2016 (selected papers)

  1. *Ohtake F, Saeki Y, Ishido S, Kanno J, *Tanaka K. (2016) The K48-K63 branched ubiquitin chain regulates NF-κB signaling. Mol Cell 64, 251-266. (Publisher link)
  2. Kincaid EZ, Murata S, Tanaka K, *Rock KL. (2016) Specialized proteasome subunits have an essential role in the thymic selection of CD8(+) T cells. Nat Immunol. 17, 938-945.
  3. Burana D, Yoshihara H, Tanno H, Yamamoto A, Saeki Y, Tanaka K, *Komada M. (2016) The Ankrd13 family of ubiquitin-interacting motif-bearing proteins regulates valosin-containing protein/p97 protein-mediated lysosomal trafficking of caveolin 1. J Biol Chem. 291, 6218-6231.
  4. Shibata Y, Tokunaga F, Goto E, Komatsu G, Gohda J, Saeki Y, Tanaka K, Takahashi H, Sawasaki T, Inoue S, Oshiumi H, Seya T, Nakano H, Tanaka Y, Iwai K, *Inoue JI. (2016) HTLV-1 Tax induces formation of the active macromolecular IKK complex by generating Lys63- and Met1-linked hybrid polyubiquitin chains. PLoS Pathog. e1006162.

2000~2015 (includes the papers of former members)

  1. Watanabe M, Takahashi H, Saeki Y, Ozaki T, Itoh S, Suzuki M, Mizushima W, Tanaka K, *Hatakeyama S. (2015) The E3 ubiquitin ligase TRIM23 regulates adipocyte differentiation via stabilization of the adipogenic activator PPARγ. eLife e05615.
  2. Sasaki K, Takada K, Ohte Y, Kondo H, Sorimachi H, Tanaka K, Takahama Y, Murata M. (2015) Thymoproteasomes produce unique peptide motifs for positive selection of CD8+ T cells. Nat Commun. 8484.
  3. Takada K, Laethem FV, Xing Y, Akane K, Suzuki H, Murata S, Tanaka K, Jameson SC, Singer A, Takahama Y. (2015) Thymus epithelium conditions antigen responsiveness in CD8+ T cells. Nat Immunol. 16, 1069-1076.
  4. Fukushima T, Yoshihara H, Furuta H, Kamei H, Hakuno F, Luan J, Duan C, Saeki Y, Tanaka K, Iemura S, Natsume T, Chida K, Nakatsu Y, Kamata H, Asano T, Takahashi SI. (2015) Nedd4-induced mono-ubiquitination of IRS-2 enhances IGF-dependent signals and mitogenic activity. Nat Commun. 7780.
  5. Yoshida Y, Saeki Y, Murakami A, Kawawaki J, Tsuchiya H, Yoshihara H, Shindo M, Tanaka K. (2015) A comprehensive method for detecting ubiquitinated substrates using TR-TUBE. Proc Natl Acad Sci USA. 12, 4630-4635.
  6. Morimoto D, Walinda E, Fukada H, Sou YS, Kageyama S, Hoshino M, Fujii T, Tsuchiya H, Saeki Y, Arita K, Ariyoshi M, Tochio H, Iwai K, Namba K, Komatsu M, Tanaka K, Shirakawa M. (2015) The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates. Nat Commun. 7116.
  7. Reincke M, Sbiera S, Hayakawa A, Theodoropoulou M, Osswald A, Beuschlein F, Meitinger T, Mizuno-Yamasaki E, Kawaguchi K, Saeki Y, Tanaka K, Wieland T, Graf E, Saeger W, Ronchi CL, Allolio B, Buchfelder M, Strom TM, Fassnacht M, Komada M. (2015) Mutations in the deubiquitinase gene USP8 cause Cushing’s disease. Nat Genet. 47, 31-38.
  8. Ohtake F, Saeki Y, Sakamoto K, Ohtake K, Nishikawa H, Tsuchiya H, Ohta T, Tanaka K, Kanno J. (2015) Ubiquitn acetylation inhibits polyubiquitin chain elongation. EMBO Rep. 16, 192-201.
  9. Pack CG, Yukii H, Toh-e A, Kudo T, Tsuchiya H, Kaiho A, Sakata E, Murata S, Yokosawa H, Sako Y, Baumeister W, Tanaka K, Saeki Y. (2014)  Quantitative live-cell imaging reveals molecular dynamics and cytoplasmic assembly of the 26S proteasome. Nat Commun. 10, 1038.
  10. Koyano F, Okatsu K, Kosako H, Tamura Y, Go E, Kimura M, Kimura Y, Tsuchiya H, Yoshihara H, Hirokawa T, Endo T, Fon EA, Trempe JF, Saeki Y, Tanaka K, Matsuda N. (2014) Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510,162-166.
  11. Yoo HM, Kang SH, Kim JY, Lee SW, Seong MW, Ka SH, Sou Y-S, Komatsu M, Tanaka K, Lee ST, Noh DY, Baek S H, Jeon YJ, and Chung CH. (2014) Modification of ASC1 by UFM1 is crucial for ERα transactivation and breast cancer development. Mol Cell 56, 1-14.
  12. Ichimura Y, Waguri S, Sou Y, Kageyama S, Hasegawa J, Ishimura R, Saito T, Yang Y, Kouno T, Fukutomi T, Hoshii T, Atsushi H, Takagi K, Mizushima T, Motohashi H, Lee M-S, Yoshimori T, Tanaka K, Yamamoto M, and Komatsu K. (2013) Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy. Mol Cell 51, 618-631.
  13. Akahane T, Sahara K, Yashiroda H, Tanaka K, and Murata S. (2013) Involvement of Bag6 and the TRC pathway in proteasome assembly. Nat Commun. 2013 Jul 31;4:2234. doi: 10.1038/ncomms3234.
  14. Sakata E, Bohn S, Mihalache O, Kiss P, Beck F, Nagy I, Nickell S, Tanaka K, Saeki Y, Förster F, and Baumeister W. (2012) Localization of the proteasomal ubiquitin receptors Rpn10 and Rpn13 by electron cryomicroscopy. Proc Natl Acad Sci USA. 109, 1479-1484.
  15. Kono K, Saeki Y, Yoshida S, Tanaka K, and Pellman D. (2012) Proteasomal degradation resolves competition between cell polarization and cellular wound healing. Cell 150, 151-164.
  16. Okatsu K, Oka T, Iguchi M, Imamura K, Kosako H, Tani N, Kimura M, Go E, Koyano F, Funayama M, Shiba-Fukushima K, Sato S, Shimizu H, Fukunaga Y, Taniguchi H, Komatsu M, Hattori N, Mihara K, Tanaka K, and Matsuda N. PINK1 autophosphorylation upon membrane potential dissipation is essential for Parkin recruitment to damaged mitochondria. (2012) Nat Commun. 3, 1016.
  17. Tokunaga F, Nakagawa T, Nakahara1 M, Saeki Y, Taniguchi M, Sakata S, Tanaka K, Nakano H, and Iwai I. (2011) Sharpin is a component of the NF-κB activating linear ubiquitin chain assembly complex. Nature 471, 633-636.
  18. Tatsumi K, Yamamoto-Mukai H, Shimizu R, Waguri S, Sou Y-S, Sakamoto A, Taya C, Shitara H, Hara T, Chung CH, Tanana K, Yamamoto M, and Komatsu M. (2011) The Ufm1-activating enzyme Uba5 is indispensable for erythroid differentiation in mice. Nat Commun.10, 1038.
  19. Sakata E, Stengel F, Fukunaga K, Zhou M, Saeki Y, Förster F, Baumeister W, Tanaka K, and Robinson CV. (2011) The catalytic activity of Ubp6 enhances maturation of the proteasomal regulatory particle. Mol Cell 42, 637-649.
  20. Komatsu M, Kurokawa H, Waguri S, Taguchi K, Kobayashi A, Ichimura Y, Sou Y-S, Ueno I, Sakamoto A, Tong K I, Kim M, Nishito Y, Iemura S, Natsume T, Ueno T, Kominami E, Motohashi H, Tanaka K, and Yamamoto M. (2010) The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. Nat Cell Biol. 12, 213-223.
  21. Tokunaga T, Sakata S, Satomi Y, Kirisako T, Kamei K, Nakagawa T, Murata S, Yamaoka S, Takao T, Tanaka K, and Iwai K. (2009) Linear ubiquitination of NEMO triggers NF-kB activation. Nat Cell Biol. 11, 123-132.
  22. Kimura Y, Yashiroda H, Kudo T, Koitabashi S, Murata S, Kakizuka A, and Tanaka K. (2009) An inhibitor of deubiquitinating enzyme regulates ubiquitin homeostasis. Cell 137, 549-559.
  23. Saeki Y, Toh-e A, Kudo T, Kawamura H, and Tanaka K. (2009) Multiple proteasome-interacting proteins assist the assembly of the yeast 19S regulatory particle. Cell 137, 900-913.
  24. Kaneko T, Hamazaki J, Iemura S, Sasaki K, Furuyama K, Natsume T, Tanaka K, and Murata S. (2009) Assembly pathway of the mammalian proteasome base subcomplex is mediated by multiple specific chaperones. Cell 137, 914-925.
  25. Yashiroda H, Mizushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Kasahara M, Kurimoto E, Sakata E, Suzuki A, Hirano Y, Murata S, Kato K, Yamane T, and Tanaka K. (2008) Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes. Nat Struct Mol Biol. 15, 228- 236.
  26. Kriegenburg F, Seeger M, Saeki Y, Tanaka K, Lauridsen A-M B, Hartmann-Petersen R, and Hendil K B. (2008) Mammalian 26S proteasomes remain intact during protein degradation. Cell 135, 355-365.
  27. Sakata E, Yamaguchi Y, Miyauchi Y, Iwai K, Chiba T, Saeki Y, Matsuda N, Tanaka K, and Kato K. (2007) Direct interactions between Nedd8 and ubiquitin E2 conjugating enzymes contribute to up- regulation of cullin-based E3 ligase activity. Nat Struct Mol Biol. 14, 167-168.
  28. Murata S, Sasaki K, Kishimoto T, Niwa S, Hayashi H, Takahama Y, and Tanaka K. (2007) Regulation of CD8+ T cell development by thymus-specific proteasomes. Science 316, 1349-1353.
  29. Komatsu M, Waguri S, Koike M, Sou Y, Ueno T, Hara T, Mizushima N, Iwata J, Ezaki J, Murata S, Hamazaki J, Nishito Y, Iemura S, Natsume N, Yanagawa T, Uwayama J, Warabi E, Yoshida H, Ishii T, Kobayashi A, Yamamoto M, Yue Z, Uchiyama Y, Kominami E, Tanaka K. (2007) Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 131, 1149-1163.
  30. Komatsu M, Waguri S, Chiba T, Murata S, Iwata J, Ueno T, Koike M, Uchiyama Y, Kominami E, Tanaka K. (2006) Loss of autophagy in the central nervous system causes neurodegeneration. Nature 441, 880-884.
  31. Hirano Y, Hayashi H, Iemura S, Hendil KB, Niwa S, Kishimoto T, Natsume T, Kasahara M, Tanaka K, Murata S. (2006) Cooperation of multiple chaperones required for the assembly of mammalian 20S proteasomes. Mol Cell 24, 977-984.
  32. Hirano Y, Hendil KB, Yashiroda H, Iemura S, Nagane R, Hioki Y, Natsume T, Tanaka K, Murata S. (2005) A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes. Nature 437, 1381-1385.
  33. Mizushima T, Hirao T, Yoshida Y, Lee S J, Chiba T, Iwai K, Yamaguchi Y, Kato K, Tsukihara T, Tanaka K. (2004) Structural basis of sugar-recognizing ubiquitin ligase. Nat Struct Mol Biol. 11, 365-370.
  34. Yoshida Y, Chiba T, Tokunaga T, Kawasaki H, Iwai K, Suzuki T, Ito Y, Matsuoka K, Yoshida M, Tanaka K, Tai T. (2002) E3 ubiquitin-ligase that recognizes sugar chains. Nature 418, 438-442.
  35. Shimura H, Hattori N, Kubo S, Mizuno Y, Asakawa S, Minoshima S, Shimizu N, Iwai K, Chiba T, Tanaka K, Suzuki S. (2000) Familial Parkinsons disease gene product, parkin, is a ubiquitin-protein ligase. Nat Genet. 25, 302-305.