Tomoki Chiba

Summary

Affiliation: Tokyo Metropolitan Institute of Medical Science
Country: Japan

Publications

  1. ncbi request reprint Loss of autophagy in the central nervous system causes neurodegeneration in mice
    Masaaki Komatsu
    Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    Nature 441:880-4. 2006
  2. pmc A new ubiquitin ligase involved in p57KIP2 proteolysis regulates osteoblast cell differentiation
    Minsoo Kim
    Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    EMBO Rep 9:878-84. 2008
  3. pmc Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice
    Masaaki Komatsu
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Cell Biol 169:425-34. 2005
  4. pmc The NEDD8 system is essential for cell cycle progression and morphogenetic pathway in mice
    K Tateishi
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Cell Biol 155:571-9. 2001
  5. ncbi request reprint Cullin-based ubiquitin ligase and its control by NEDD8-conjugating system
    Tomoki Chiba
    Laboratory of Frontier Science, The Tokyo Metropolitan Institute of Medical Science, Tokyo 113 8613, Japan
    Curr Protein Pept Sci 5:177-84. 2004
  6. ncbi request reprint Fbs2 is a new member of the E3 ubiquitin ligase family that recognizes sugar chains
    Yukiko Yoshida
    Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Biol Chem 278:43877-84. 2003
  7. ncbi request reprint Excess peroxisomes are degraded by autophagic machinery in mammals
    Jun ichi Iwata
    Department of Biochemistry, Juntendo University School of Medicine, Bunkyo ku, Tokyo, Japan
    J Biol Chem 281:4035-41. 2006
  8. pmc A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier
    Masaaki Komatsu
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo, Japan
    EMBO J 23:1977-86. 2004
  9. ncbi request reprint DDB2, the xeroderma pigmentosum group E gene product, is directly ubiquitylated by Cullin 4A-based ubiquitin ligase complex
    Noriyuki Matsuda
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    DNA Repair (Amst) 4:537-45. 2005
  10. ncbi request reprint [Regulation of the protein degradation pathway by the ubiquitin family: its implication in neurodegenerative diseases]
    Tomoki Chiba
    The Tokyo Metropolitan Institute of Medical Science, Laboratory of Frontier Science
    Rinsho Shinkeigaku 45:976-8. 2005

Collaborators

Detail Information

Publications43

  1. ncbi request reprint Loss of autophagy in the central nervous system causes neurodegeneration in mice
    Masaaki Komatsu
    Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    Nature 441:880-4. 2006
    ..Our results indicate that autophagy is essential for the survival of neural cells, and that impairment of autophagy is implicated in the pathogenesis of neurodegenerative disorders involving ubiquitin-containing inclusion bodies...
  2. pmc A new ubiquitin ligase involved in p57KIP2 proteolysis regulates osteoblast cell differentiation
    Minsoo Kim
    Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    EMBO Rep 9:878-84. 2008
    ..As overexpression of p57(KIP2) promoted osteoblast differentiation, these results indicate the importance of FBL12 and the degradation of p57(KIP2) in the regulation of osteoblast cell differentiation...
  3. pmc Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice
    Masaaki Komatsu
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Cell Biol 169:425-34. 2005
    ..Our results indicate the important role of autophagy in starvation response and the quality control of proteins and organelles in quiescent cells...
  4. pmc The NEDD8 system is essential for cell cycle progression and morphogenetic pathway in mice
    K Tateishi
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Cell Biol 155:571-9. 2001
    ..Thus, the NEDD8 system is essential for the regulation of protein degradation pathways involved in cell cycle progression and morphogenesis, possibly through the function of the Cul family proteins...
  5. ncbi request reprint Cullin-based ubiquitin ligase and its control by NEDD8-conjugating system
    Tomoki Chiba
    Laboratory of Frontier Science, The Tokyo Metropolitan Institute of Medical Science, Tokyo 113 8613, Japan
    Curr Protein Pept Sci 5:177-84. 2004
    ..This review summarizes recent advances in biochemical and genetic studies on how the NEDD8-modifying system regulates Cul-family proteins and their physiology...
  6. ncbi request reprint Fbs2 is a new member of the E3 ubiquitin ligase family that recognizes sugar chains
    Yukiko Yoshida
    Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    J Biol Chem 278:43877-84. 2003
    ..Thus, Fbs2 is a novel member of F-box protein family that recognizes N-glycans and plays a role in ERAD...
  7. ncbi request reprint Excess peroxisomes are degraded by autophagic machinery in mammals
    Jun ichi Iwata
    Department of Biochemistry, Juntendo University School of Medicine, Bunkyo ku, Tokyo, Japan
    J Biol Chem 281:4035-41. 2006
    ..This is the first direct evidence for the contribution of autophagic machinery in peroxisomal degradation in mammals...
  8. pmc A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier
    Masaaki Komatsu
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo, Japan
    EMBO J 23:1977-86. 2004
    ..Ufm1, Uba5, and Ufc1 are all conserved in metazoa and plants but not in yeast, suggesting its potential roles in various multicellular organisms...
  9. ncbi request reprint DDB2, the xeroderma pigmentosum group E gene product, is directly ubiquitylated by Cullin 4A-based ubiquitin ligase complex
    Noriyuki Matsuda
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    DNA Repair (Amst) 4:537-45. 2005
    ..We also showed that an amino acid substitution, K244E, in DDB2 derived from a XP-E patient did not affect its ubiquitylation...
  10. ncbi request reprint [Regulation of the protein degradation pathway by the ubiquitin family: its implication in neurodegenerative diseases]
    Tomoki Chiba
    The Tokyo Metropolitan Institute of Medical Science, Laboratory of Frontier Science
    Rinsho Shinkeigaku 45:976-8. 2005
    ..This review highlighted the recent progress in our understanding on the regulation of UPP and its cooperation with AP for the quality control of the proteins and elimination of ubiquitin positive aggregates...
  11. ncbi request reprint CHIP: a quality-control E3 ligase collaborating with molecular chaperones
    Shigeo Murata
    Department of Molecular Oncology, Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, 113 8613, Tokyo, Japan
    Int J Biochem Cell Biol 35:572-8. 2003
    ..Accumulating evidence from in vitro studies indicates that this is apparently the case. Here, we present and discuss several unresolved but critical issues related to the molecular mechanism and in vivo roles of CHIP...
  12. ncbi request reprint [Biology of the reversible protein ubiquitination]
    Tomoki Chiba
    The Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Seikagaku 77:537-44. 2005
  13. ncbi request reprint Conditional knockdown of proteasomes results in cell-cycle arrest and enhanced expression of molecular chaperones Hsp70 and Hsp40 in chicken DT40 cells
    Tomoko Tanahashi-Hori
    Department of Molecular Oncology, The Tokyo Metropolitan Institute of Medical Science, 3 18 22 Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    J Biol Chem 278:16237-43. 2003
    ..Our Z(-/-/-)/Z-HA cell line would be useful for evaluating proteolytic processes catalyzed by the proteasome in many biological events in vertebrate cells...
  14. doi request reprint Muscle RING-finger protein-1 (MuRF1) as a connector of muscle energy metabolism and protein synthesis
    Suguru Koyama
    Department of Enzymatic Regulation for Cell Functions Calpain Project, Tokyo Metropolitan Institute of Medical Science Rinshoken, Tokyo 113 8613, Japan
    J Mol Biol 376:1224-36. 2008
    ....
  15. ncbi request reprint [Physiological role in constitutive autophagy]
    Masaaki Komatsu
    Tanpakushitsu Kakusan Koso 51:1515-8. 2006
  16. ncbi request reprint In vitro systems for NEDD8 conjugation by Ubc12
    Tomoki Chiba
    Laboratory of Frontier Science, The Tokyo Metropolitan Institute of Medical Science, Honkomagome, Bunkyo ku, Tokyo 113 8613, Japan
    Methods Enzymol 398:68-73. 2005
    ..This chapter describes methods for the purification of NEDD8 conjugation enzymes and in vitro Nedd8 conjugation...
  17. ncbi request reprint Depletion of hsp90beta induces multiple defects in B cell receptor signaling
    Fumika Shinozaki
    Department of Biophysics and Biochemistry, and Undergraduate Program for Bioinformatics and Systems Biology, Graduate School of Science, The University of Tokyo, Bunkyo ku, Tokyo 113 0033, Japan
    J Biol Chem 281:16361-9. 2006
    ..Unexpectedly, however, introducing the Hsp90alpha gene is also effective in restoration; thus, these defects might be caused by a reduction in the total expression of Hsp90 rather than by loss of Hsp90beta-specific function...
  18. ncbi request reprint E3 ubiquitin ligase that recognizes sugar chains
    Yukiko Yoshida
    Department of Tumor Immunology, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613, Japan
    Nature 418:438-42. 2002
    ..Our results indicate that SCF(Fbx2) ubiquitinates N-glycosylated proteins that are translocated from the ER to the cytosol by the quality control mechanism...
  19. ncbi request reprint BTB domain-containing speckle-type POZ protein (SPOP) serves as an adaptor of Daxx for ubiquitination by Cul3-based ubiquitin ligase
    Jeong Eun Kwon
    NRL of Protein Biochemistry, School of Biological Sciences, Seoul National University, Seoul 151 742, Korea
    J Biol Chem 281:12664-72. 2006
    ..These results suggest that SPOP/Cul3-ubiquitin ligase plays an essential role in the control of Daxx level and, thus, in the regulation of Daxx-mediated cellular processes, including transcriptional regulation and apoptosis...
  20. ncbi request reprint The ubiquitin-proteasome system plays essential roles in presenting an 8-mer CTL epitope expressed in APC to corresponding CD8+ T cells
    Xuefeng Duan
    Department of Microbiology and Immunology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
    Int Immunol 18:679-87. 2006
    ..Thus, application of the ubiquitin-fusion degradation pathway was useful even in immunization with genes encoding a single CTL epitope for induction of specific and active CD8+ T cells...
  21. ncbi request reprint [NEDD8 conjugation system]
    Tomoki Chiba
    Tanpakushitsu Kakusan Koso 51:1206-9. 2006
  22. ncbi request reprint SUMO-specific protease SUSP4 positively regulates p53 by promoting Mdm2 self-ubiquitination
    Moon Hee Lee
    NRL of Protein Biochemistry, School of Biological Sciences, Seoul National University, Seoul 151 742, Korea
    Nat Cell Biol 8:1424-31. 2006
    ..UV damage induced SUSP4 expression, leading to an increase in p53 levels in parallel with a decrease in Mdm2 levels. These findings establish a new mechanism for the elevation of cellular p53 levels in response to UV damage...
  23. ncbi request reprint Direct interactions between NEDD8 and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity
    Eri Sakata
    Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3 1 Tanabe dori, Mizuho ku, Nagoya 467 8603, Japan
    Nat Struct Mol Biol 14:167-8. 2007
    ..Our data imply that NEDD8 forms an active platform on the SCF complex for selective recruitment of ubiquitin-charged E2s in collaboration with RBX1, and thereby upregulates the E3 activity...
  24. pmc SCRAPPER-dependent ubiquitination of active zone protein RIM1 regulates synaptic vesicle release
    Ikuko Yao
    Mitsubishi Kagaku Institute of Life Sciences MITILS, 11 Minamiooya, Machida, Tokyo 194 8511, Japan
    Cell 130:943-57. 2007
    ..Thus, SCRAPPER has an essential function in regulating proteasome-mediated degradation of RIM1 required for synaptic tuning...
  25. ncbi request reprint Allele-selective effect of PA28 in MHC class I antigen processing
    Taketoshi Yamano
    Laboratory for Immunochaperones, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Tsurumi, Yokohama, Japan
    J Immunol 181:1655-64. 2008
    ....
  26. pmc Ubiquitin-fusion degradation pathway plays an indispensable role in naked DNA vaccination with a chimeric gene encoding a syngeneic cytotoxic T lymphocyte epitope of melanocyte and green fluorescent protein
    Manxin Zhang
    Department of Microbiology and Immunology, Graduate School of Medical Sciences, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka 812 8582, Japan
    Immunology 112:567-74. 2004
    ..It is noteworthy to document that genetic immunization with pGFP plus pTRP-2(181-188) failed to exert the antitumour immunity...
  27. ncbi request reprint The involvement of immunoproteasomes in induction of MHC class I-restricted immunity targeting Toxoplasma SAG1
    Kazunari Ishii
    Department of Parasitology, Graduate School of Medical Sciences, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka 812 8582, Japan
    Microbes Infect 8:1045-53. 2006
    ....
  28. ncbi request reprint TBP-interacting protein 120B (TIP120B)/cullin-associated and neddylation-dissociated 2 (CAND2) inhibits SCF-dependent ubiquitination of myogenin and accelerates myogenic differentiation
    Seiji Shiraishi
    Department of Biology, Faculty of Science, Chiba University, Chiba 263 8522, Japan
    J Biol Chem 282:9017-28. 2007
    ..TIP120B is proposed to be a novel regulator for myogenesis...
  29. pmc Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2
    Akira Kobayashi
    Center for Tsukuba Advanced Research Alliance, Institute of Basic Medical Sciences, and JST ERATO Environmental Response Project, University of Tsukuba, Tsukuba 305 8575, Japan
    Mol Cell Biol 24:7130-9. 2004
    ..To our knowledge, Nrf2 and Keap1 are the first reported mammalian substrate and adaptor, respectively, of the Cul3-based E3 ligase system...
  30. ncbi request reprint Expression of HIV-1 accessory protein Vif is controlled uniquely to be low and optimal by proteasome degradation
    Mikako Fujita
    Department of Virology, The University of Tokushima, Graduate School of Medicine, 3 18 15 Kuaramoto cho, Tokushima shi Tokushima 770 8503, Japan
    Microbes Infect 6:791-8. 2004
    ..Vif was unique in its short half-life and in the magnitude of the degradation. Taken together, we conclude that the proteasome degradation of HIV-1 Vif is a virologically important process and crucial for the function of Vif...
  31. ncbi request reprint Multiple roles of Rbx1 in the VBC-Cul2 ubiquitin ligase complex
    Yuzuru Megumi
    Department of Molecular Cell Biology, Graduate School of Medicine, Osaka City University, 1 4 3 Asahi machi, Abeno Ku, Osaka 545 8585, Japan
    Genes Cells 10:679-91. 2005
    ..Taken together, these results indicate that various mechanisms regulate both the activities and the stability of cullin-based ligases...
  32. pmc Ligand-dependent switching of ubiquitin-proteasome pathways for estrogen receptor
    Yukiyo Tateishi
    Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki, Japan
    EMBO J 23:4813-23. 2004
    ..One pathway is necessary for the transactivation of the receptor and the other is involved in the quality control of the receptor...
  33. ncbi request reprint A palmitoylated RING finger ubiquitin ligase and its homologue in the brain membranes
    Kazuaki Araki
    Department of Molecular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
    J Neurochem 86:749-62. 2003
    ..In agreement, Sakura associating with the membrane was specifically palmitoylated. Although the molecular targets of their Ub ligation remain to be identified, these findings imply a novel function of the palmitoylated E3 Ub ligase(s)...
  34. ncbi request reprint Structural basis of sugar-recognizing ubiquitin ligase
    Tsunehiro Mizushima
    Precursory Research for Embryonic Science and Technology PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332 0012, Japan
    Nat Struct Mol Biol 11:365-70. 2004
    ....
  35. ncbi request reprint Dioxin receptor is a ligand-dependent E3 ubiquitin ligase
    Fumiaki Ohtake
    ERATO, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama 332 0012, Japan
    Nature 446:562-6. 2007
    ....
  36. ncbi request reprint Isolation and characterization of phage-displayed single chain antibodies recognizing nonreducing terminal mannose residues. 1. A new strategy for generation of anti-carbohydrate antibodies
    Keiko Sakai
    Institute of Glycotechnology, Tokai University, Kanagawa 259 1292, Japan
    Biochemistry 46:253-62. 2007
    ..Further studies on the purification and characterization of these scFvs are presented in an accompanying paper in this issue...
  37. ncbi request reprint Common anti-apoptotic roles of parkin and alpha-synuclein in human dopaminergic cells
    Yutaka Machida
    Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
    Biochem Biophys Res Commun 332:233-40. 2005
    ..Our findings indicate that both parkin and alpha-SN share a common pathway in DA metabolism whose abnormality leads to accumulation of oxidative DA metabolites and subsequent cell death...
  38. ncbi request reprint Decline of striatal dopamine release in parkin-deficient mice shown by ex vivo autoradiography
    Shigeto Sato
    Department of Neurology, Juntendo University School of Medicine, Bunkyo, Tokyo, Japan
    J Neurosci Res 84:1350-7. 2006
    ..Our results suggest that dopaminergic neurons could behave abnormally before neuronal death...
  39. pmc Two distinct pathways mediated by PA28 and hsp90 in major histocompatibility complex class I antigen processing
    Taketoshi Yamano
    Department of Molecular Medicine, Division of Immunology, Nagasaki University School of Medicine, Nagasaki 852 8523, Japan
    J Exp Med 196:185-96. 2002
    ..Thus, these two pathways operate either redundantly or specifically, depending on antigen species and cell type...
  40. ncbi request reprint Differential expression regulation of the alpha and beta subunits of the PA28 proteasome activator in mature dendritic cells
    Ferry Ossendorp
    Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
    J Immunol 174:7815-22. 2005
    ..Therefore, maturation of DC not only improves costimulation but also MHC class I processing. This mechanism enhances the CD8(+) CTL (cross)-priming capacity of mature DC...
  41. ncbi request reprint The fusion oncoprotein PML-RARalpha induces endoplasmic reticulum (ER)-associated degradation of N-CoR and ER stress
    Md Matiullah Khan
    Laboratory of Molecular Genetics, RIKEN Tsukuba Institute, 3 1 1 Koyadai, Tsukuba, Ibaraki 305 0074, Japan
    J Biol Chem 279:11814-24. 2004
    ..Overexpression of N-CoR induces the differentiation of APL-derived NB4 cells, suggesting that the low levels of N-CoR in the nucleus may contribute at least partly to PML-RARalpha-mediated leukemogenesis...
  42. pmc 14-3-3eta is a novel regulator of parkin ubiquitin ligase
    Shigeto Sato
    Department of Neurology, Juntendo University School of Medicine, Bunkyo, Tokyo, Japan
    EMBO J 25:211-21. 2006
    ..Our findings indicate that 14-3-3eta is a regulator that functionally links parkin and alpha-SN. The alpha-SN-positive and 14-3-3eta-negative control of parkin activity sheds new light on the pathophysiological roles of parkin...
  43. pmc Proteasome activator PA28gamma-dependent nuclear retention and degradation of hepatitis C virus core protein
    Kohji Moriishi
    Research Center for Emerging Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita Shi, Osaka 565 0871, Japan
    J Virol 77:10237-49. 2003
    ..Overexpression of PA28gamma enhanced the proteolysis of the HCV core protein. Thus, the nuclear retention and stability of the HCV core protein is regulated via a PA28gamma-dependent pathway through which HCV pathogenesis may be exerted...